Selectively targeted antimicrobial peptides and the use thereof

ABSTRACT

The present invention relates to targeting peptides capable of specifically binding to microbial organisms (e.g.,  P. aeruginosa  or  S. mutans ), antimicrobial peptides having antimicrobial activities, and specifically/selectively targeted antimicrobial peptides (STAMPs). In addition, the present invention provides methods of selectively killing or inhibiting microbial organisms by using the peptides or compositions provided by the present invention.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a Continuation of U.S. patent Ser. No. 14/178,061,filed on Feb. 11, 2014, now U.S. Pat. No. 9,351,490, issued on May 31,2016, which is a Continuation of U.S. patent application Ser. No.12/938,278, filed on Nov. 2, 2010, now U.S. Pat. No. 8,680,058, issuedon Mar. 25, 2014, which is a Continuation of U.S. patent applicationSer. No. 11/851,372, filed on Sep. 6, 2007, now U.S. Pat. No. 7,846,895,issued on Dec. 7, 2010, which claims priority to U.S. ProvisionalApplication No. 60/842,871 filed on Sep. 6, 2006, all of which areincorporated herein by reference.

FIELD OF INVENTION

The present invention relates to the field of antimicrobial compositionsand treatment.

BACKGROUND OF THE INVENTION

The indigenous microflora found at human mucosal surfaces are criticalfor acquiring nutrients and providing protective colonization againstpathogenic microorganisms. When the normal flora are disrupted by anynumber of factors, the result is often microbial infections at themucosal surface, many of which affect populations worldwide. The lack ofa robust immune response at mucosal surfaces has limited the prescribingclinician to conventional antibiotics or antimicrobials for treatment ofmucosal infections. Unfortunately for the normal flora, most smallmolecule antibiotics have broad spectrum of activity, killing benign andpathogenic organisms indiscriminately. This effect often leads to severeantibiotic associated infections due to the vacated niche available forpathogen colonization. Clostridium difficile, Candida albicans andStaphylococcus aureus are examples of classical opportunistic pathogensthat take advantage of increased niche size after antibiotic treatment.The problems resulting from wide-spectrum antibiotic use, combined withthe emergence of drug-resistant strains, highlight the fundamental needfor new “targeted” antibiotic therapies to combat mucosal pathogens witha minimal impact on normal microflora.

Previous efforts toward achieving target-specific antimicrobial therapyconsisted of conjugating antibiotics to monoclonal antibodies orconstructing large fusion proteins with bactericidal and bacterialrecognition domains (Qiu et al., 2005). Neither method has yet to resultin functional, effective therapeutics due to the low efficiency ofchemical conjugation, instability of large proteins, or high cost ofproduction.

Although G10KHc, a specifically targeted antimicrobial peptide (STAMP),has been developed and demonstrated increased killing potency,selectivity and kinetics against targeted bacteria (Eckert et al.,2006), there is a need to develop novel STAMPs that are capable ofspecifically or selectively killing or inhibiting the growth ofundesirable target microorganisms.

SUMMARY OF THE INVENTION

One aspect of the present invention relates to aselectively/specifically targeted antimicrobial peptide (STAMP) whichcomprises a targeting peptide and an antimicrobial peptide. The STAMPfurther comprises a linker peptide.

In one embodiment, the targeting peptide is selected from the groupconsisting of C16 or CSP_(C16) (TFFRLFNRSFTQALGK, SEQ ID NO. 2), M8 orCSP_(M8) (TFFRLFNR, SEQ ID NO 5), and peptide 1903 (NIFEYFLE, SEQ ID NO10).

In another embodiment, the linker peptide is selected from the groupconsisting of GGG (SEQ ID NO17), AAA (SEQ ID NO 18), SAT (SEQ ID NO 19),ASA (SEQ ID NO 20), SGG (SEQ ID NO 21), PYP (SEQ ID NO 22), SGS (SEQ IDNO 23), GGS (SEQ ID NO 24), SPS(SEQ ID NO 25), PSGSP (SEQ ID NO 26),PSPSP (SEQ ID NO 27), GGSGGS (SEQ ID NO 28) or a combination (amultimer) of any two (dimer), three (timer), four (tetramer), five(pentamer) or more than five thereof.

In another embodiment, the antimicrobial peptide is selected from thegroup consisting of G2 (a derivative of novispirin G10,KNLRRIIRKGIHIIKKY* as shown in SEQ ID NO 3) (* denotes C-terminalamidation), S6L3-33 having an amino acid sequence of FKKFWKWFRRF (SEQ IDNO 7) and BD2.21 having an amino acid sequence of KLFKFLRKHLL (SEQ ID NO11).

In another embodiment, the STAMP comprises a targeting peptide and anantimicrobial peptide, wherein the targeting peptide is covalentlylinked to the antimicrobial peptide via a peptide bond, wherein thetargeting peptide is selected from the group consisting of C16 (SEQ IDNO 2), M8 (SEQ ID NO 5), and 1903 (SEQ ID NO10); and wherein theantimicrobial peptide is selected from the group consisting of G2 (SEQID NO 3), S6L3-33 (SEQ ID NO 7) and BD2.21 (SEQ ID NO 11).

In another embodiment, the STAMP comprises a targeting peptide which iscovalently linked to a linker peptide via a peptide bond and anantimicrobial peptide which is covalently linked to the linker peptidevia a peptide bond, wherein the targeting peptide is selected from thegroup consisting of C16 (SEQ ID NO 2), M8 (SEQ ID NO 5), and 1903 (SEQID NO10); wherein the antimicrobial peptide is selected from the groupconsisting of G2 (SEQ ID NO 3), S6L3-33 (SEQ ID NO 7) and BD2.21 (SEQ IDNO 11); and wherein the peptide linker is selected from the groupconsisting of GGG (SEQ ID NO 17), AAA (SEQ ID NO 18), SAT (SEQ ID NO19), ASA (SEQ ID NO 20), SGG (SEQ ID NO 21), PYP (SEQ ID NO 22), SGS(SEQ ID NO 23), GGS (SEQ ID NO 24), SPS(SEQ ID NO 25), PSGSP (SEQ ID NO26), PSPSP (SEQ ID NO 27), and GGSGGS (SEQ ID NO 28).

In another embodiment, the STAMP is selected from the group consistingof C16G2 (SEQ ID NO. 4); C16-33 (SEQ ID NO. 8); C16-BD2.21 (SEQ ID NO.14); M8G2 (SEQ ID NO. 15); M8-33 (SEQ ID NO. 9); M8-BD2.21 (SEQ ID NO.6); 1903-G2 (SEQ ID NO. 12); 1903-33 (SEQ ID NO. 16); and 1903-BD2.21(SEQ ID NO. 13).

In another embodiment, the amino acids in the STAMP are D-amino acidenantiomer.

Another aspect of the present invention relates to a STAMP compositioncomprising a STAMP and an antibiotic, wherein the STAMP compositionshows a synergistic antimicrobial effect in killing or reducing thegrowth of a target microbial organism. In one embodiment, the STAMP isG10KHc (SEQ ID NO 36). In another embodiment, the antibiotic istobramycin. In a preferred embodiment, the STAMP composition comprisesG10KHc (SEQ ID NO 36) and tobramycin.

Another aspect of the present invention relates to a STAMP compositioncomprising a STAMP and an agent which can enhance, maintain, orfacilitate the function or activity of the STAMP. In one embodiment, theagent is a protease inhibitor or rhDNase. In a preferred embodiment, theSTAMP composition comprises G10KHc (SEQ ID NO 36) and a proteaseinhibitor and/or rhDNase.

Another aspect of the present invention is a diagnostic agent comprisinga targeting peptide and a detectable agent. In one embodiment, thetargeting peptide is conjugated to the detectable agent.

Another aspect of the present invention relates to the use of acomposition of the present invention (e.g., the STAMP or the STAMPcomposition) in selectively killing, inhibiting or reducing the growthof a target microbial organism in a subject or on a biofilm or treatinga disease associated with a target microbial organism.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: Selective killing activity of C16G2 against S. mutans. S.mutans, S. sanguinis, and S. gordonii planktonic cells were exposed to25 μM of the STAMP C16G2, or its untargeted parent antimicrobial peptideG2, for 1 min. Surviving cfu/mL were detected and compared. Datarepresent averages from at least 3 independent experiments.

FIG. 2: Inhibitory activity of G2 and C16G2 against single-speciesbiofilms. S. gordonii (A), S. sanguinis (B) and S. mutans (C)monoculture biofilms were grown and then exposed for 1 min to 25 μMSTAMP or STAMP component (as indicated in the figure), washed, andregrown with fresh medium. Biofilm recovery was monitored over time byOD₆₀₀. Data represent averages from 3 independent experiments.

FIG. 3: C16G2 activity against S. mutans within a multi-species biofilm.Mixed cultures of S. mutans, S. sanguinis, and S. gordonii were allowedto form a biofilm in saliva and were then exposed to 25 μM C16G2,CSP_(C16), or G2. After washing, the biofilms were allowed to recover infresh medium/saliva. The regrowth of the biofilm over time was monitoredby measuring absorbance at OD₆₀₀, while the health of the S. mutanswithin the biofilm was measured by luciferase activity (RLU production).The data were plotted as RLU/OD₆₀₀ and represent averages of at least 3independent experiments.

FIG. 4: Activity of M8G2 against oral bacteria in biofilms. S. mutans(A) or S. sanguinis (B) single-species biofilms were mock-treated orexposed to 25 μM M8G2 (specified in the figure). After removal of theSTAMP and the addition of fresh medium, biofilm recovery was monitoredover time by monitoring absorbance at OD₅₀₀. The data represent theaverage of 3 independent experiments.

FIG. 5: Biofilm inhibitory activity of S6L3-33 and S6L3-33-containingSTAMPs. Single-species biofilms of S. mutans (A) or S. sanguinis (B)were treated with M8-33, C16-33 or S6L3-33 alone (specified in thefigure) for 1 min. After agent removal and stringent washing, theregrowth of the biofilms was tracked over 4 h by measuring absorbance atOD₆₀₀ after the addition of fresh medium. The data represent an averagevalue obtained from at least 3 independent assays.

FIG. 6: HPLC and MALDI spectra for G10KHc. The quality of purifiedG10KHc was assessed by HPLC (a) and MALDI mass spectrometry (b). Bymonitoring UV 215, a single peak was detected during HPLC (at 10.06 mL)that had the correct mass for G10KHc (4267.44).

FIG. 7: Antimicrobial kinetics of G10KHc, G10, and tobramycin. P.aeruginosa strain ATCC 15692 was either mock treated or challenged withthe STAMP G10KHc, untargeted G10, or tobramycin (10 μM) and thesurviving cfu/mL quantitated after 1 min, 5 min, 30 min and 2 h. Theassay was conducted in 30% mouse serum and represents the average of atleast three independent experiments.

FIG. 8: Time-kill assay against high-density planktonic P. aeruginosa.Cultures (1×10⁸ cfu/mL) were exposed to 5 μM G10KHc or G10 with andwithout equal molar tobramycin co-treatment, as well as administeredtobramycin alone. After 24 h, surviving cfu/mL were determined byplating. Data points represent the averages of three independentexperiments.

FIG. 9: Enhanced antimicrobial activity of G10KHc and tobramycin againstbiofilm P. aeruginosa. Biofilms were grown on disk reactors andchallenged with 100 μg/mL of agent as indicated. After 4 and 24 h,surviving bacteria were harvested and plated for quantitation from atleast 3 independent experiments.

* indicates that the number of cfu/mL from G10KHc/tobramycin treatedcultures was too small to appear on the log scale.

FIG. 10: Dye uptake mediated by sub-inhibitory concentrations of G10KHc.(a) P. aeruginosa were treated with medium (left column) or 2 μM G10KHc(right column) for 5 min followed by PI dye addition. Bright-field(upper panel) and fluorescence (lower panel) images of the same fieldwere collected and evaluated for intracellular dye accumulation (redfluorescence). (b) Surviving cfu/mL from untreated (dye only) andG10KHc-treated cultures were quantitated after visualization and platedas 5-fold serial dilution.

FIG. 11: Activity and stability of G10KHc and G10KHc-D in sputum. (A)Exogenously added P. aeruginosa were challenged with 25 μM G10KHc (withor without PMSF), 25 μM G10KHc-D, or left untreated (specified in thefigure), and the surviving cfu/mL rescued and quantitated 4 h afteragent addition. Rescued cfu/mL were expressed as the average of threeindependent experiments with standard deviations. (B) G10KHc (with andwithout PMSF, specified in the figure) was added to sputum for specificdurations and peptide stability (milli-absorbance units, mAU) wasmonitored by HPLC. The increasing mobile phase linear gradient is shownin black. (**) Intact G10KHc identified by MALDI mass spectrometry atretention volume 10.29 mL. (*) Fractions collected for antimicrobialanalysis (Table 1).

FIG. 12: Effect of rhDNase on G10KHc and G10KHc-D activity inconcentrated sputum. Minimally diluted pooled sputum samples withexogenously added P. aeruginosa were treated with 25 μM G10KHc (withPMSF) or 50 μM G10KHc-D for 1 h after pretreatment with or withoutrhDNase. Rescued cells were quantitated and expressed as the percentageof input cfu/mL. The data represent the average of at least 3independent experiments with standard deviation.

FIG. 13: Killing of single-species Streptococcus mutans mature biofilmswith C16-BD2.21 and 1903-BD2.21. The figure indicates that C16-BD2.21and 1903-BD2.21 can kill 33% and 15% of the viable S. mutans within themature biofilm (grown 18-24 h) respectively, after the biofilm wastreated by the peptides for only 20 min.

FIG. 14: Impact of C16-BD2.21 and 1903-BD2.21 on multi-species biofilmof oral Streptococci. (A) shows that C16-BD2.21 has no impact on thetotal cfu/mL population and 1903-BD2.21 reduced total population byabout 30%. (B) shows that ratio of surviving S. mutans to totalStreptococci was 0.075 under C16-BD2.21 treatment and the ratio wasabout 0.2 under 1903-BD2.21 treatment.

DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS

One aspect of the present invention relates to selectively/specificallytargeted antimicrobial peptides (STAMPs) and the use thereof.

The term “selectively/specifically targeted antimicrobial peptide” or“STAMP” refers to a chimeric polypeptide which comprises a targetingpeptide and an antimicrobial peptide, wherein the targeting peptide iscovalently linked or conjugated (e.g., via a peptide bond) to theantimicrobial peptide either at the C-terminal or N-terminal of thetargeting peptide. For example, one STAMP may comprise one of thefollowing two structures: 1) a targeting peptide with its C-terminalcovalently linked to the N-terminal of an antimicrobial peptide [Aminoterminus-targeting peptide-peptide bond-antimicrobial peptide-carboxylterminus], and 2) an antimicrobial peptide with its C-terminalcovalently linked to the N-terminal of a targeting peptide [Aminoterminus-antimicrobial peptide-peptide bond-targeting peptide-carboxylterminus].

In one embodiment of the present invention, the STAMP further comprisesa peptide linker by which the targeting peptide is covalently linked orconjugated to the antimicrobial peptide. In this case, a STAMP maycomprise one of the following two structures: 1) a targeting peptidewith its C-terminal covalently linked to the N-terminal of a linkerpeptide and an antimicrobial peptide with its N-terminal covalentlylinked to the C-terminal of the linker peptide (Amino terminus-targetingpeptide-peptide bond-linker peptide-antimicrobial peptide-peptidebond-carboxyl terminus) and 2) a targeting peptide with its N-terminalcovalently linked to the C-terminal of a linker peptide and anantimicrobial peptide with its C-terminal covalently linked to theN-terminal of the linker peptide (Amino terminus-antimicrobialpeptide-peptide bond-linker peptide-peptide bond-targetingpeptide-carboxyl terminus).

According to the present invention, a targeting peptide can be anysuitable peptide which recognizes or binds to a target (e.g., a targetcell, a target tissue, a target microbial organism). Particularly, atargeting peptide specifically interacts with or specifically recognizesa target, through, for example, the cell surface appendages such asflagella and pili, and surface exposed proteins, lipids andpolysaccharides of a target. In one embodiment, a targeting peptidespecifically recognizes or interacts with only one or a few target(s)while minimally recognizing or interacting with non-target(s). Inanother embodiment, a targeting peptide can be a peptide capable ofspecifically binding to a microorganism, e.g., a target microbialorganism.

In one embodiment, the targeting peptide provided by the presentinvention can be identified via screening peptide libraries. Forexample, a phage display peptide library can be screened against atarget microbial organism or a desired antigen or epitope thereof. Inparticular, phage display peptide libraries (e.g., Ph.D 7, Ph.D. 12,Ph.D C7C libraries from New England Biolabs) that contain >10⁹ uniquerandom-peptide-sequence-containing phage clones. The Ph.D.-C7C librarydisplays 7-mer peptides with disulfide linkages, while the Ph.D.-7 andPh.D.-12 libraries contain completely randomized 7-mer and 12-merresidues, respectively. The M13 filamentous phage used for the procedurecarried the random insert as an N-terminal fusion to the minor coatprotein pIII. In screening a targeting peptide that specificallyrecognizes a target or target microbial organism, 10¹⁰ pfu/ml of phagelibrary was incubated with 10⁹ microbial organisms (e.g., bacterialcells) for which targeting peptides are desired. After centrifugation,unbound phage was removed by aspiration. The pellet, which contained thetarget microbial organisms with the bound phage, was washed severaltimes using buffers containing mild detergent to remove loosely boundphage particles, and the tightly bound phage particles were eluted. Thisprocess is termed panning. The eluted phage was amplified by infectingE. coli F⁺ strains. After 3-4 rounds of panning and amplification, aphage pool was obtained, which contained clones with high bindingaffinity for the bacteria that it was panned against. Ten to twentyphage clones from this pool were randomly picked for DNA sequencing,from which the amino acid sequence of the peptide insert was determined.By aligning the amino acid sequence of multiple clones from the samephage pool, a consensus sequence for the binding/targeting peptide wasconstructed. This consensus sequence represents one of thebinding/targeting peptides specific for the particular microbialorganism. To confirm the binding specificity of the consensus peptide,the peptide was chemically synthesized and conjugated to a dye (e.g.,FITC, a green fluorescence dye). The labeled peptide was incubated withthe microbial organism and analyzed by fluorescent microscopy for targetmicrobial species-specific binding. This methodology ensured thatpeptides selected from phage display exhibit the same bindingspecificity as a free peptide independent of the M13 phage particle.

The targeting peptide of the present invention can also be a peptideobtained based on rational design. For example, one can design atargeting peptide based on the biochemical and biophysicalcharacteristics of amino acids and the surfaces of microorganisms. Ingeneral, positively charged peptides are likely to bind negativelycharged components on the cell surface and vice versa. Similarly,hydrophobic peptides may bind to hydrophobic pockets on the cell surfacebased on hydrophobic interactions while the secondary or tertiarystructure of a peptide may fit into certain structures on the surface ofa microorganism.

A peptide identified through a screening or design method can be used asa targeting peptide for specifically recognizing a target microbialorganism. Examples of such targeting peptide are disclosed in U.S.patent application Ser. No. 10/706,391 (U.S. Pub. No. 20040137482),which include, for example, 1) targeting peptides capable ofspecifically binding to or recognizing Pseudomonas, especially P.aeruginosa (e.g., targeting peptides 12:1, 12:2, 12:3, 12:4, 12:5, 12:6,12:7, 12:8; 12:9, and 12:10); 2) targeting peptides capable ofspecifically binding to Staphylococcus, especially S. aureus (e.g.,targeting peptides SA5:1, SA5:3, SA5:4, SA5:5, SA5:6, SA5:7, SA5:8,SA5:9, SA5:10, SA2:2, SA2:4, SA2:5, SA2:6, SA2:7, SA2:8, SA2:9, SA2:10,and SA2:11); and 3) targeting peptides capable of specifically bindingto E. coli (e.g., targeting peptides DH5.1, DH5.2, DH5.3, DH5.4, DH5.5,DH5.6, DH5.7, DH5.8, and DH5.9).

In one embodiment of the present invention, targeting peptidesspecifically binding to or recognizing Pseudomonas, especially P.aeruginosa, include, for example, cat-1 (or KH) domain, KKH (SEQ ID NO31). Targeting peptides specifically binding to or recognizingStreptococci include, for example, bacterial pheromones such as CSP(SGSLSTFFRLFNRSFTQALGK, SEQ ID NO 1), CSP 1 (EMRLSKFFRDFILQRKK, SEQ IDNO 29) and CSP2 (EMRISRIILDFLFLRKK, SEQ ID NO 30) and fragments thereof.Further, targeting peptides specifically binding to or recognizing S.pneumoniae include, for example, CSP1 and CSP2. Targeting peptidesspecifically binding to or recognizing S. mutans include, for example,CSP, C16 or CSP_(C16) (TFFRLFNRSFTQALGK, SEQ ID NO 2), M8 or CSP_(M8)(TFFRLFNR, SEQ ID NO 5), and peptide 1903 (NIFEYFLE, SEQ ID NO 10).

The targeting peptides provided by the present invention can benaturally or non-naturally occurring peptides. For example, thetargeting peptides provided by the present invention can berecombinantly made, chemically synthesized, or naturally existing. Inone embodiment, the targeting peptide contains an amino acid sequencethat naturally exists (e.g., CSP, CSP 1 and CSP2). In anotherembodiment, the targeting peptide contains an amino acid sequence thatconstitutes an internal part of a naturally occurring polypeptide (e.g.,C16 and M8 in the present invention). In another embodiment, thetargeting peptide contains an amino acid sequence encoded by a sequencenaturally existing in a genome and such amino acid sequence is notadjacent to any amino acid sequence naturally adjacent to it, e.g., suchamino acid sequence is adjacent to a heterologous sequence in thetargeting peptide.

The targeting peptide provided by the present invention can also includea peptide having an amino acid sequence that is derived or modified froma targeting amino acid sequence specifically illustrated in the presentinvention, provided that the derived or modified sequence stillmaintains or has an enhanced specificity with respect to its targetmicrobial organism. For example, the targeting amino acid sequence canbe structurally modified via deletion, mutation, addition of amino acidsor other structural entities, or any other structural changes as long asthese changes do not alter or adversely affect the binding ability ofthe targeting amino acid sequence to its target microbial organism.

The targeting peptide according to the present invention specificallyinteracts with or binds to the target organism (e.g., through theexternal surface of the organism) via different molecular interactionssuch as ionic interaction, Vander Waals forces, ligand-receptorinteraction, or hydrophobic interaction. For example, the targetingpeptide of the present invention can also be a peptide ligand, receptor,or fragment thereof that specifically recognizes a target microbialorganism. In one example, the targeting peptide of the present inventioncan be a glucan binding protein of Streptococcus mutans that canspecifically bind insoluble glucans on the surface of S. mutans. Foranother example, the targeting peptides can be a bacterial pheromone ora fragment thereof.

The targeting peptide according to the present invention comprises about4 to about 40 amino acids, from about 5 to about 30, or from about 6 toabout 20. In one preferred embodiment, the targeting peptide has alength of 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22,23, 24, 25, 26, 27, 28, 29, or 30 amino acids.

It is contemplated that the targeting peptides includes peptides whichspecifically bind a target cell or tissue (e.g., a plant call, an animalcell, or fungal organism). The examples of these targeting peptidesinclude Chitinase, Lectins, and targeting fragments thereof.

The targeting peptide according to the present invention can be producedby any suitable method known to one skilled in the art by itself or incombination with a linker peptide and an antimicrobial peptide. Forexample, the targeting peptides can be chemically synthesized via asynthesizer or recombinantly made using an expression system, e.g., abacterial, yeast, or eukaryotic cell expression system. In the chemicalsynthesis, the targeting peptide can be made by L-amino acid enantiomersor D-amino acid enantiomers. It is observed that the targeting peptideconsisting of D-enantiomers increases the stability without compromisingthe activity of the targeting peptide.

The linker peptide according to the present invention is a peptide thatcan be used to connect a targeting peptide to an antimicrobial peptidewithout interfering or reducing the activity of the targeting peptide orthe antimicrobial peptide. The peptide linker is from about 2 to 20amino acids, from 2 to 12, or from 3 to 12 amino acids. Examples of thepeptide linkers include, for example, GGG (SEQ ID NO 17), AAA (SEQ ID NO18), SAT (SEQ ID NO 19), ASA (SEQ ID NO 20), SGG (SEQ ID NO 21), PYP(SEQ ID NO 22), SGS (SEQ ID NO 23), GGS (SEQ ID NO 24), SPS(SEQ ID NO25), PSGSP (SEQ ID NO 26), PSPSP (SEQ ID NO 27), or a combination (amultimer) of any two (dimer), three (trimer), four (tetramer), five(pentamer) or more than five of the listed peptide linkers. In oneembodiment, the linker peptide is GGG (SEQ ID NO 17). In anotherembodiment, the linker peptide is a dimmer of GGS (SEQ ID NO 24), whichis GGSGGS (SEQ ID NO 28).

The linker peptide according to the present invention can be produced byany suitable method known to one skilled in the art by itself or incombination with a targeting peptide and an antimicrobial peptide. Forexample, the linker peptides can be chemically synthesized via asynthesizer or recombinantly made using an expression system, e.g., abacterial, yeast, or eukaryotic cell expression system. In the chemicalsynthesis, the linker peptide can be made by L-amino acid enantiomers orD-amino acid enantiomers. It is observed that peptides consisting ofD-enantiomers increase the stability without comprising the activity ofthe peptides.

The antimicrobial peptide according to the present invention is apeptide capable of killing a microbial organism or inhibiting itsgrowth. The antimicrobial activities of the antimicrobial peptides ofthe present invention include, without limitation, antibacterial,antiviral, or antifungal activities. Antimicrobial peptides includevarious classes of peptides, e.g., peptides originally isolated fromplants as well as animals. In animals, antimicrobial peptides areusually expressed by various cells including neutrophils and epithelialcells. In mammals including human, antimicrobial peptides are usuallyfound on the surface of the tongue, trachea, and upper intestine.Naturally occurring antimicrobial peptides are generally amphipathicmolecules that contain fewer than 100 amino acids. Many of thesepeptides generally have a net positive charge (i.e., cationic) and mostform helical structures.

In one embodiment, the antimicrobial peptide according to the presentinvention comprises about 2 to about 100 amino acids, from about 5 toabout 50, or from about 7 to about 20. In one preferred embodiment, thetargeting peptide has a length of 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 amino acids.

In another embodiment, the antimicrobial peptide has the antimicrobialactivity with a minimum inhibitory concentration (MIC) of no more thanabout 40 μM, no more than about 30 μM, no more than 20 μM, or no morethan 10 μM.

In another embodiment, the antimicrobial peptides include those listedin Table 7 (SEQ ID Nos 34-35 and 54-97). In another embodiment, theantimicrobial peptide contains one or more antimicrobial peptidesincluding, without limitation, alexomycin, andropin, apidaecin,bacteriocin, β-pleated sheet bacteriocin, bactenecin, buforin,cathelicidin, α-helical clavanin, cecropin, dodecapeptide, defensin,β-defensin, α-defensin, gaegurin, histatin, indolicidin, magainin,melittin, nisin, novispirin G10, protegrin, ranalexin, tachyplesin, andderivatives thereof.

Among these known antimicrobial peptides, tachyplesins are known to haveantifungal and antibacterial activities. Andropin, apidaecin, bactencin,clavanin, dodecappeptide, defensin, and indolicidin are antimicrobialpeptides having antibacterial activities. Buforin, nisin and cecropinpeptides have been demonstrated to have antimicrobial effects onEscherichia. coli, Shigella disenteriae, Salmonella typhimurium,Streptococcus pneumoniae, Staphylococcus aureus, and Pseudomonasaeroginosa. Magainin and ranalexin peptides have been demonstrated tohave antimicrobial effects on the same organisms, and in addition havesuch effects on Candida albicans, Cryptococcus neoformans, Candidakrusei, and Helicobacter pylori. Magainin has also been demonstrated tohave antimicrobial effects on herpes simplex virus. Alexomycin peptideshave been demonstrated to have antimicrobial effects on Campylobacterjejuni, Moraxella catarrhalis and Haemophilus inflluenzae while defensinand β-pleated sheet defensin peptides have been shown to haveantimicrobial effects on Streptococcus pneumoneae. Histatin peptides andthe derivatives thereof are another class of antimicrobial peptides,which have antifungal and antibacterial activities against a variety oforganisms including Streptococcus mutans (MacKay, B. J. et al., Infect.Immun. 44:695-701 (1984); Xu, et al., J. Dent. Res. 69:239 (1990)).

In one embodiment, the antimicrobial peptide of the present inventioncontains one or more antimicrobial peptides from a class of histatinpeptides and the derivatives thereof. For example, the antimicrobialpeptide of the present invention contains one or more derivatives ofhistatin including, without limitation, histatin 5 having an amino acidsequence of DSHAKRHHGY KRKFHEKHHS HRGY (SEQ ID NO 32) or dhvar-1 havingan amino acid sequence of KRLFKELKFS LRKY (SEQ ID NO 33).

In another embodiment, the antimicrobial peptide of the presentinvention contains one or more antimicrobial peptides from a class ofprotegrins and the derivatives thereof. For example, the antimicrobialpeptide of the present invention contains protegrin PG-1 having an aminoacid sequence of RGGRLCYCRRRFCVCVGR (SEQ ID NO 3334). The protegrinpeptides have been shown to have antimicrobial effects on Streptococcusmutans, Neisseria gonorrhoeae, Chlamydia trachomatis and Haempohilusinfluenzae. Protegrin peptides are described in U.S. Pat. Nos.5,693,486, 5,708,145, 5,804,558, 5,994,306, and 6,159,936, all of whichare incorporated herein by reference.

In yet another embodiment, the antimicrobial peptide of the presentinvention contains one or more antimicrobial peptides from a class ofnovispirin and the derivatives thereof for treating cariogenicorganisms, e.g., Streptococcus mutans or Pseudomonas aeroginosa. Forexample, the antimicrobial peptide of the present invention includesnovispirin G10 having an amino acid sequence KNLRRIIRKGIHIIKKYG (SEQ IDNO 35) and G2 (a derivative of novispirin G10) which has one C-terminalamino acid deletion, and one internal deletion from G10 and an amidatedC-terminus having the amino acid sequence of KNLRIIRKGIHIIKKY* (SEQ IDNO 3) (* denotes C-terminal amidation).

In yet another embodiment, the antimicrobial peptide of the presentinvention contains peptides rationally designed and tested to possessthe antimicrobial activity against a microbial organism (e.g.,Streptococcus mutans). The examples of these peptides include, withoutany limitation, S6L3-33 having an amino acid sequence of FKKFWKWFRRF(SEQ ID NO 7) and BD2.21 having an amino acid sequence of KLFKFLRKHLL(SEQ ID NO 11).

The antimicrobial peptide according to the present invention can beproduced by any suitable method known to one skilled in the art byitself or in combination with a targeting peptide and a linker peptide.For example, the antimicrobial peptides can be chemically synthesizedvia a synthesizer or recombinantly made using an expression system,e.g., a bacterial, yeast, or eukaryotic cell expression system. In thechemical synthesis, the antimicrobial peptide can be made by L-arninoacid enantiomers or D-amino acid enantiomers.

In yet another embodiment, the STAMP comprises a targeting peptide andan antimicrobial peptide, wherein the targeting peptide is covalentlylinked to the antimicrobial peptide via a peptide bond, wherein thetargeting peptide is selected from the group consisting of C16 (SEQ IDNO 2), M8 (SEQ ID NO 5), and 1903 (SEQ ID NO 10); and wherein theantimicrobial peptide is selected from the group consisting of G2 (SEQID NO 3), S6L3-33 (SEQ ID NO 7) and BD2.21 (SEQ ID NO 11).

In yet another embodiment, the STAMP comprises a targeting peptide whichis covalently linked to a linker peptide via a peptide bond and anantimicrobial peptide which is covalently linked to the linker peptidevia a peptide bond, wherein the targeting peptide is selected from thegroup consisting of C16 (SEQ ID NO 2), M8 (SEQ ID NO 5), and 1903 (SEQID NO 10); wherein the antimicrobial peptide is selected from the groupconsisting of G2 (SEQ ID NO 3), S6L3-33 (SEQ ID NO 7) and BD2.21 (SEQ IDNO 11). In yet another embodiment, the peptide linker is selected fromthe group consisting of GGG (SEQ ID NO 17), AAA (SEQ ID NO 18), SAT (SEQID NO 19), ASA (SEQ ID NO 20), SGG (SEQ ID NO 21), PYP (SEQ ID NO 22),SGS (SEQ ID NO 23), GGS (SEQ ID NO 24), SPS (SEQ ID NO 25), PSGSP (SEQID NO 26), PSPSP (SEQ ID NO 27), and GGSGGS (SEQ ID NO 28). Examples ofsuch STAMPs include but are not limited to the STAMPS listed in Table 1:C16G2 (SEQ ID NO 4); C16-33 (SEQ ID NO 8); C16-BD2.21 (SEQ ID NO 14);M8G2 (SEQ ID NO 6); M8-33 (SEQ ID NO 9); M8-BD2.21 (SEQ ID NO 15);1903-G2 (SEQ ID NO 12); 1903-33 (SEQ ID NO 16); and 1903-BD2.21 (SEQ IDNO 13).

Another aspect of the present invention relates to a compositioncomprising a plurality of STAMPS, wherein the composition comprises afirst STAMP and a second STAMP and the first STAMP is different from thesecond STAMP. In one embodiment, the first STAMP comprises a firsttargeting peptide covalently linked to a first antimicrobial peptide viaa peptide bond. The second STAMP comprises a second targeting peptidecovalently linked to a second antimicrobial peptide via a peptide bond.The difference between the first STAMP and the second STAMP is such thatat least one corresponding moiety of the two STAMPs is different fromeach other. For example, in one embodiment, the first targeting peptideis different from the second targeting peptide or the firstantimicrobial peptide is different from the second antimicrobialpeptide. In another embodiment, the first targeting peptide is differentfrom the second targeting peptide and the first antimicrobial peptide isdifferent from the second antimicrobial peptide.

In another embodiment, the first STAMP comprises a first targetingpeptide which is covalently linked to a first linker peptide via apeptide bond and a first antimicrobial peptide which is covalentlylinked to the first linker peptide via a peptide bond. The second STAMPcomprises a second targeting peptide which is covalently linked to asecond linker peptide via a peptide bond and a second antimicrobialpeptide which is covalently linked to the second linker peptide via apeptide bond. The difference between the first STAMP and the secondSTAMP is such that at least one corresponding moiety of the two STAMPsis different from each other. For example, in one embodiment, the firsttargeting peptide is different from the second targeting peptide (thefirst linker peptide is the same as the second linker peptide and thefirst antimicrobial peptide is the same as the second antimicrobialpeptide); or the first linker peptide is different from the secondpeptide linker; or the first antimicrobial peptide is different from thesecond antimicrobial peptide. In another embodiment, the first targetingpeptide is the same as the second targeting peptide (the first linkerpeptide is different from the second linker peptide and the firstantimicrobial peptide is different from the second antimicrobialpeptide); or the first peptide linker is the same as the second peptidelinker; or the first antimicrobial peptide is the same the secondantimicrobial peptide. In another embodiment, the first targetingpeptide is different from the second targeting peptide, the first linkerpeptide is different from the second peptide linker; and the firstantimicrobial peptide is different from the second antimicrobialpeptide.

The STAMP of the present invention can be made by any suitable meansknown to one skilled in the art. In one embodiment, a nucleotidesequence encoding the STAMP can be synthesized through a DNA synthesizeror a nucleotide sequence encoding a targeting peptide can be ligated toa nucleotide sequence encoding an antimicrobial peptide moiety, eitherdirectly or via a nucleotide sequence encoding a peptide linker. Thenucleotide can be expressed in an appropriate expression system, e.g., acommercially available bacterial, yeast, or eukaryotic cell expressionsystem. In the chemical synthesis, the STAMP can be made by L-amino acidenantiomers or D-amino acid enantiomers. It is observed that the STAMPconsisting of D-enantiomers increases the stability without comprisingthe activity of the STAMP.

Another aspect of the present invention relates to a STAMP compositioncomprising a STAMP and an antibiotic. A synergistic antimicrobial effecthas been unexpectedly observed when a STAMP is co-administered with anantibiotic in killing or reducing the growth of a target microbialorganism. Antibiotics suitable for co-administration with the STAMPinclude substances, produced synthetically or naturally, which caninhibit the growth of or kill microbial organisms. Such antibioticsinclude, without any limitation, β-lactam antibiotics (e.g., ampicillin,aziocillin, aztreonam, carbenicillin, cefoperazone, ceftriaxone,cephaloridine, cephalothin, cloxacillin, moxalactam, penicillin,piperacillin, and ticarcillin), amoxicillin, bacitracin,chloramphenicol, clindamycin, capreomycin, colistimethate,ciprofloxacin, doxycycline, erythromycin, fusidic acid, fosfomycin,fusidate sodium, gramicidin, gentamycin, lincomycin, minocycline,macrolides, monobactams, nalidixic acid, novobiocin, ofloxcin,rifamycins, tetracyclines, vancomycin, tobramycin, and trimethoprim. Inone example, the STAMP composition comprises a G10KHc STAMP (SEQ ID NO36) and tobramycin and exhibits a synergistic enhancement ofantimicrobial activity to P. aeruginosa in both biofilms and planktoniccultures.

Another aspect of the present invention relates to a STAMP compositioncomprising a STAMP and an agent which can enhance, maintain, orfacilitate the function or activity of the STAMP. In one embodiment, thechemical is a protease inhibitor. The STAMP composition is exposed to aprotease-present environment where the presence of the protease mayreduce the antimicrobial activity of the STAMP via, for example,enzymatic degradation. The combination of a protease inhibitor and aSTAMP stabilizes the STAMP from the protease degradation and thusenhance the activity of the STAMP. The protease-present environmentincludes, for example, body fluid (e.g., urine, blood, serum, salvia,sputum, mucosal fluid). The protease includes, for example, neutrophilelastase, proteinase-3, cycteine protease, metalloprotease,serine-protease, or other proteases derived from bacteria and/or hosts.The protease inhibitor includes, for example, BMF, EDTA, PMFS,benzamidine, and/or recombinant α-1 antitrypsin (rAAT).

In yet another embodiment, the agent is human DNase. One example of theSTAMP composition is the combination of a STAMP (G10KHc (SEQ ID NO 36)and a DNase. The composition was used to reduce P. areruginosa in sputumand exhibited enhanced antimicrobial activity of G10KHc, as the DNasereduced sputum viscosity and enhanced the STAMP diffusion.

Another aspect of the present invention relates to a pharmaceuticalcomposition comprising a STAMP and a suitable pharmaceutical carrier.The term “pharmaceutically acceptable carrier” as used herein means apharmaceutically-acceptable material, composition or vehicle, such as aliquid or solid filler, diluent, excipient, solvent or encapsulatingmaterial, involved in carrying or transporting a STAMP from onelocation, body fluid, tissue, organ, or portion of the body, to anotherlocation, body fluid, tissue, organ, or portion of the body. Eachcarrier must be “pharmaceutically acceptable” in the sense of beingcompatible with the other ingredients, e.g., a STAMP, of the formulationand suitable for use in contact with the tissue or organ of humans andanimals without excessive toxicity, irritation, allergic response,immunogenicity, or other problems or complications, commensurate with areasonable benefit/risk ratio. Some examples of materials which canserve as pharmaceutically-acceptable carriers include: (1) sugars, suchas lactose, glucose and sucrose; (2) starches, such as corn starch andpotato starch; (3) cellulose, and its derivatives, such as sodiumcarboxymethyl cellulose, ethyl cellulose and cellulose acetate; (4)powdered tragacanth; (5) malt; (6) gelatin; (7) talc; (8) excipients,such as cocoa butter and suppository waxes; (9) oils, such as peanutoil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil andsoybean oil; (10) glycols, such as propylene glycol; (1) polyols, suchas glycerin, sorbitol, mannitol and polyethylene glycol; (12) esters,such as ethyl oleate and ethyl laurate; (13) agar; (14) bufferingagents, such as magnesium hydroxide and aluminum hydroxide; (15) alginicacid; (16) pyrogen-free water; (17) isotonic saline; (18) Ringer'ssolution; (19) ethyl alcohol; (20) phosphate buffer solutions; and (21)other non-toxic compatible substances employed in pharmaceuticalformulations.

Another aspect of the present invention is a diagnostic agent comprisinga targeting peptide and a detectable agent. The diagnostic agent of thisinvention can be useful in diagnostic assays, e.g., for detecting thepresence or amount of a target or target microbial organism in a placewhere the target organism is susceptible to exist (e.g., tissues,organs, body fluid, sputum, surface of a body or organ, mucosal surface,implant, biofilm, or serum, device, air, fluid, cell culture, surface ofan industry article or a device), or for detecting the onset,development, or remission of a condition (e.g., an infection or adisease) associated with the target microorganism.

In one embodiment, the targeting peptide typically will be labeled withor conjugated to a detectable agent. Numerous detectable agents areavailable which can be generally grouped into the following categories:

(a) Radioisotopes, such as ³⁵S, ¹⁴C, ¹³C, ¹⁵N, ¹²⁵I, ³H, and ¹³¹I. Thepeptide can be labeled with the radioisotope using the techniques knownin the art and radioactivity can be measured using scintillationcounting; in addition, the peptide can be spin labeled for electronparamagnetic resonance for carbon and nitrogen labeling.

(b) Fluorescent agents such as BODIPY, BODIPY analogs, rare earthchelates (europium chelates), fluorescein and its derivatives, FITC, 5,6carboxyfluorescein, rhodamine and its derivatives, dansyl, Lissamine,phycoerythrin, green fluorescent protein, yellow fluorescent protein,red fluorescent protein and Texas Red. Fluorescence can be quantifiedusing a fluorometer.

(c) Various enzyme-substrate agents, such luciferases (e.g., fireflyluciferase and bacterial luciferase), luciferin,2,3-dihydrophthalazinediones, malate dehydrogenase, urease, peroxidasesuch as horseradish peroxidase (HRPO), alkaline phosphatase,β-glucoamylase, lysozyme, saccharide oxidases (e.g., glucose oxidase,galactose oxidase, and glucose-6-phosphate dehydrogenase), heterocyclicoxidases (such as uricase and xanthine oxidase), lactoperoxidase,microperoxidase, and the like. Examples of enzyme-substrate combinationsinclude, for example: (i) Horseradish peroxidase (HRPO) with hydrogenperoxidase as a substrate, wherein the hydrogen peroxidase oxidizes adye precursor (e.g., orthophenylene diamine (OPD) or3,3′,5,5′-tetramethyl benzidine hydrochloride (TMB)); (ii) alkalinephosphatase (AP) with para-Nitrophenyl phosphate as chromogenicsubstrate; and (iii) β-D-galactosidase (β-D-Gal) with a chromogenicsubstrate (e.g., p-nitrophenyl-β-D-galactosidase) or fluorogenicsubstrate 4-methylumbelliferyl-β-D-galactosidase.

In another embodiment, the detectable agent is not necessarilyconjugated to the targeting peptide but is capable of recognizing thepresence of the targeting peptide and the agent can be detected. Forexample, the detectable agent is an antibody that specifically binds tothe targeting peptide. The antibody can then be detected or quantifiedthrough various methods known in the art (See Harlow & Lane,Antibodies—A Laboratory Manual (1988)).

In another embodiment, the diagnostic agent of the present invention canbe provided in a kit, i.e., a packaged combination of reagents inpredetermined amounts with instructions for performing the diagnosticassay. Where the targeting peptide is labeled with an enzyme, the kitwill include substrates and cofactors required by the enzyme (e.g., asubstrate precursor which provides the detectable chromophore orfluorophore). In addition, other additives may be included such asstabilizers, buffers (e.g., a block buffer or lysis buffer) and thelike. The relative amounts of the various reagents may be varied widelyto provide for concentrations in solution of the reagents whichsubstantially optimize the sensitivity of the assay. Particularly, thereagents may be provided as dry powders, usually lyophilized, includingexcipients which on dissolution will provide a reagent solution havingthe appropriate concentration.

According to another aspect of the present invention, the compositions(e.g., the STAMPs or the STAMP compositions) of the present inventioncan be used to kill, inhibit or reduce the growth of a target microbialorganism to which the targeting peptide specifically binds.

In one embodiment, the compositions of the present invention provideantimicrobial effect to a target microbial organism and can be used totreat a disease or infection associated with the target microbialorganism. An antimicrobial effect includes inhibiting the growth orkilling of the target microbial organisms, or interfering with anybiological functions of the target microbial organisms. In general, thecompositions of the present invention can be used to treat a disease orinfection at any place in a host, e.g., at any tissue including surfacesof any tissue or implant. In one embodiment, the compositions are usedto specifically kill or inhibit planktonic target microbial organisms inbody fluid (e.g., blood, sputum). In one embodiment, the compositions ofthe present invention are used to treat a disease or infection on amucosal surface or a surface containing a biofilm.

The term “biofilm” refers to an accumulation of microbial organisms thatproduce an extracellular polysaccharide and proteinaceous material thatact as a natural glue to immobilize or embed the organisms. Biofilms mayform on solid biological or non-biological surfaces. A biofilmconsisting essentially of non-harmful, non-pathogenic, commensalmicrobial organisms is essential for maintaining a healthy and normalmicrobial flora to prevent the invasion and establishment of otherpathogenic microbial organisms, e.g., yeast infection. However, if themicroorganism population in a biofilm is disturbed by overpopulation ofpathogenic microbial organisms (e.g., cariogenic organisms likeStreptococcus mutans), the resulting biofilm may lead tobiofilm-associated microbial infection. Examples of biofilm-associatedmicrobial infections include infections of oral soft tissues, teeth anddental implants; middle ear; gastrointestinal tract; urogenital tract;airway/lung tissue; eye; urinary tract prostheses; peritoneal membraneand peritoneal dialysis catheters, indwelling catheters for hemodialysisand for chronic administration of chemotherapeutic agents (Hickmancatheters); cardiac implants such as pacemakers, prosthetic heartvalves, ventricular assist devices, and synthetic vascular grafts andstents; prostheses, internal fixation devices, and percutaneous sutures;and tracheal and ventilator tubing. Both indwelling and subcutaneousbiomedical implants or devices are potential sites for microbial orboilfilm-based infections and represent important targets for thecontrol of infection, inflammation, and the immune response. Biomedicalsystems such as blood oxygenators, tracheal lavage, dental water units,and dialyzers are also susceptible to bacterial contamination andbiofilm formation.

In yet another embodiment, the composition of present invention can beused to disturb the balance of pathogen-containing biofilm (e.g., abiofilm overpopulated by pathogenic microbial organisms) such thatundesirable, pathogenic microbial organisms (target microbial organisms)are selectively killed, inhibited or reduced and the desirable,non-pathogenic microbial populations (non-target microbial organisms)are minimally impacted. The composition can be used in many places in ananimal or human body which have mucosal surfaces colonized by multiplespecies microbial biofilms. Examples of these places include mouth,vagina, gastrointestinal (GI) tract, esophageal tract, respiratorytract, implants. For example, in human mouth there usually exist manydifferent microbes including yeasts and bacteria. Most of the bacteriaare non-harmful commensal bacteria. Administering the composition of thepresent invention targets specifically to, for example, cariogenicorganisms (e.g. Streptococcus mutans) and will have minimum effect onnon-targeted microbial organisms, and thus will not have an undesirableeffect on non-targeted microbial organisms.

The composition of the present invention can also be used to inhibittarget microbial organisms or apply to various biofilm surfaces outsideof a human body, e.g., industrial articles or applications. For example,in food processing industry the composition of the present invention canbe administered to food processing equipments or food itself to preventinfections related to food consumption, e.g., Salmonella in a poultryprocessing facility.

The target microbial organism of the present invention can be anybacteria, rickettsia, fungi, yeasts, protozoa, or parasites. In oneembodiment, the target microbial organism is a cariogenic organism,e.g., Streptococcus mutans. In another embodiment, the target microbialorganisms of the present invention include, without limitation,Escherichia coli, Candida, Salmonella, Staphylococcus, and Pseudomonas,especially Campylobacter jejuni, Candida albicans, Candida krusei,Chlamydia trachomatis, Clostridium difficile, Cryptococcus neoformans,Haempohilus influenzae, Helicobacter pylor, Moraxella catarrhalis,Neisseria gonorrhoeae, Pseudomonas aeroginosa, Salmonella typhimurium,Shigella disenteriae, Staphylococcus aureus, and Streptococcuspneumoniae.

For example, S. mutans infection is commonly found in mouth and causesdental caries. Porphyromonas gingivalis, various Actinomyces species,spirochetes, and black-pigmented bacteroides are commonly associatedwith infections of gingival and surrounding connective tissues, whichcause periodontal diseases. Streptococcus pneumoniae, Haemophiliusinfluenza, or Moraxella cararrhalis infections are commonly found inacute otitis media (AOM) and otitis media effusion (OME) ascomplications of upper respiratory infections in young children.

Helicobacter pylori (H. pylori) bacteria are found in the gastric mucouslayer or adherent to the epithelial lining of the stomach, and causemore than 90% of duodenal ulcers and up to 80% of gastric ulcers. OtherGI tract infections include, without limitation, campylobacter bacterialinfection, primarily Campylobacter jejuni associated with diarrhea,cholera caused by Vibrio cholerae serogroups, salmonellosis caused bybacteria salmonella such as S. typhimurium and S. enteritidis,shigellosis caused by bacteria Shigella, e.g., Shigella dysenteriae andtraveler's diarrhea caused by enterotoxigenic Escherichia coli (ETEC).Clostridium difficile infection is also commonly found in thegastrointestinal tract or esophageal tract.

Pseudomonas organisms have been associated with common-source nosocomialoutbreaks; in addition, they have been incriminated in bacteremia,endocarditis, and osteomyelitis in narcotic addicts. Infections withPseudomonas organisms can also occur in the ear, lung, skin, or urinarytract of patients, often after the primary pathogen has been eradicatedby antibiotics. Serious infections are almost invariably associated withdamage to local tissue or with diminished host resistance. Patientscompromised by cystic fibrosis and those with neutropenia appear atparticular risk to severe infection with P. aeruginosa. Prematureinfants; children with congenital anomalies and patients with leukemia;patients with burns; and geriatric patients with debilitating diseasesare likely to develop Pseudomonas infections. The organism is prevalentin urine receptacles and on catheters, and on the hands of hospitalstaff.

The staphylococci, of which Staphylococcus aureus is the most importanthuman pathogen, are hardy, gram-positive bacteria that colonize the skinof most human beings. If the skin or mucous membranes are disrupted bysurgery or trauma, staphylococci may gain access to and proliferate inthe underlying tissues, giving rise to a typically localized,superficial abscess. Although these cutaneous infections are mostcommonly harmless, the multiplying organisms may invade the lymphaticsand the blood, leading to the potentially serious complications ofstaphylococcal bacteremia.

These complications include septic shock and serious metastaticinfections, including endocarditis, arthritis, osteomyelitis, pneumonia,and abscesses in virtually any organ. Certain strains of S. aureusproduce toxins that cause skin rashes or that mediate multisystemdysfunction, as in toxic shock syndrome. Coagulase-negativestaphylococci, particularly S. epidermidis, are important nosocomialpathogens, with a particular predilection for infecting vascularcatheters and prosthetic devices. S. saprophyticus is a common cause ofurinary tract infection.

Yeast or Candida infections (Candidiasis) typically occur either orally(Oropharyngeal Candida or OPC) or vaginally (Vulvovaginal Candida orVVC). Candidiasis is caused by a shift in the local environment thatallows Candida strains (most commonly Candida albicans) already presenton skin and on mucosal surfaces such as mouth and vagina to multiplyunchecked. Gonorrhea, chlamydia, syphilis, and trichomoniasis areinfections in the reproductive tract, which cause sexually transmitteddiseases, e.g., pelvic inflammatory disease.

Administration of the compositions according to the present invention.The STAMP or the STAMP composition can be administered to a subject byany administration route known in the art, including without limitation,oral, enteral, buccal, nasal, topical, rectal, vaginal, aerosol,transmucosal, epidermal, transdermal, ophthalmic, pulmonary, and/orparenteral administration. A parenteral administration refers to anadministration route that typically relates to injection which includesbut is not limited to intravenous, intramuscular, intraarterial,intrathecal, intracapsular, intraorbital, intra cardiac, intradermal,intraperitoneal, transtracheal, subcutaneous, subcuticular,intraarticular, subcapsular, subarachnoid, intraspinal, and/orintrasternal injection and/or infusion.

The STAMP or the STAMP composition can be given to a subject in the formof formulations or preparations suitable for each administration route.The formulations useful in the methods of the present invention includeone or more STAMPs, one or more pharmaceutically acceptable carrierstherefor, and optionally other therapeutic ingredients. The formulationsmay conveniently be presented in unit dosage form and may be prepared byany methods well known in the art of pharmacy. The amount of activeingredient which can be combined with a carrier material to produce asingle dosage form will vary depending upon the subject being treatedand the particular mode of administration. The amount of a STAMP whichcan be combined with a carrier material to produce a pharmaceuticallyeffective dose will generally be that amount of a STAMP which produces atherapeutic effect. Generally, out of one hundred percent, this amountwill range from about 1 percent to about ninety-nine percent of theSTAMP, preferably from about 5 percent to about 70 percent.

Methods of preparing these formulations or compositions include the stepof bringing into association a STAMP with one or more pharmaceuticallyacceptable carriers and, optionally, one or more accessory ingredients.In general, the formulations are prepared by uniformly and intimatelybringing into association a STAMP with liquid carriers, or finelydivided solid carriers, or both, and then, if necessary, shaping theproduct.

Formulations suitable for oral administration may be in the form ofcapsules, cachets, pills, tablets, lozenges (using a flavored basis,usually sucrose and acacia or tragacanth), powders, granules, or as asolution or a suspension in an aqueous or nonaqueous liquid, or as anoil-in-water or water-in-oil liquid emulsion, or as an elixir or syrup,or as pastilles (using an inert base, such as gelatin and glycerin, orsucrose and acacia) and/or as mouth washes and the like, each containinga predetermined amount of a STAMP as an active ingredient. A compoundmay also be administered as a bolus, electuary, or paste. For example,in one embodiment, the compositions of the present invention are used totreat or prevent cariogenic organism infections, e.g., S. mutansinfection associated with dental caries and are prepared as additives tofood or any products having direct contact to an oral environment,especially an oral environment susceptible to dental caries. To treat orprevent dental caries one or more compositions of the present inventioncan be formulated into a baby formula, mouthwash, lozenges, gel,varnish, toothpaste, toothpicks, tooth brushes, or other tooth cleansingdevices, localized delivery devices such as sustained release polymersor microcapsules, oral irrigation solutions of any kind whethermechanically delivered or as oral rinses, pacifiers, and any foodincluding, without limitation, chewing gums, candies, drinks, breads,cookies, and milk.

In solid dosage forms for oral administration (e. g., capsules, tablets,pills, dragees, powders, granules and the like), the STAMP is mixed withone or more pharmaceutically-acceptable carriers, such as sodium citrateor dicalcium phosphate, and/or any of the following: (1) fillers orextenders, such as starches, lactose, sucrose, glucose, mannitol, and/orsilicic acid; (2) binders, such as, for example, carboxymethylcellulose,alginates, gelatin, polyvinyl pyrrolidone, sucrose and/or acacia; (3)humectants, such as glycerol; (4) disintegrating agents, such asagar-agar, calcium carbonate, potato or tapioca starch, alginic acid,certain silicates, and sodium carbonate, (5) solution retarding agents,such as paraffin, (6) absorption accelerators, such as quaternaryammonium compounds; (7) wetting agents, such as, for example, acetylalcohol and glycerol monostearate; (8) absorbents, such as kaolin andbentonite clay; (9) lubricants, such a talc, calcium stearate, magnesiumstearate, solid polyethylene glycols, sodium lauryl sulfate, andmixtures thereof; and (10) coloring agents. In the case of capsules,tablets and pills, the pharmaceutical compositions may also comprisebuffering agents. Solid compositions of a similar type may also beemployed as fillers in soft and hard-filled gelatin capsules using suchexcipients as lactose or milk sugars, as well as high molecular weightpolyethylene glycols and the like.

A tablet may be made by compression or molding, optionally with one ormore accessory ingredients. Compressed tablets may be prepared usingbinder (for example, gelatin or hydroxypropylmethyl cellulose),lubricant, inert diluent, preservative, disintegrant (for example,sodium starch glycolate or cross-linked sodium carboxymethyl cellulose),surface-active or dispersing agent. Molded tablets may be made bymolding in a suitable machine a mixture of the powdered peptide orpeptidomimetic moistened with an inert liquid diluent. Tablets, andother solid dosage forms, such as dragees, capsules, pills and granules,may optionally be scored or prepared with coatings and shells, such asenteric coatings and other coatings well known in thepharmaceutical-formulating art. They may also be formulated so as toprovide slow or controlled release of a STAMP therein using, forexample, hydroxypropylmethyl cellulose in varying proportions to providethe desired release profile, other polymer matrices, liposomes and/ormicrospheres. They may be sterilized by, for example, filtration througha bacteria-retaining filter, or by incorporating sterilizing agents inthe form of sterile solid compositions which can be dissolved in sterilewater, or some other sterile injectable medium immediately before use.These compositions may also optionally contain pacifying agents and maybe of a composition that they release the STAMP(s) only, orpreferentially, in a certain portion of the gastrointestinal tract,optionally, in a delayed manner. Examples of embedding compositionswhich can be used include polymeric substances and waxes. The STAMP canalso be in micro-encapsulated form, if appropriate, with one or more ofthe above-described excipients.

Liquid dosage forms for oral administration include pharmaceuticallyacceptable emulsions, microemulsions, solutions, suspensions, syrups andelixirs. In addition to the STAMP, the liquid dosage forms may containinert diluents commonly used in the art, such as, for example, water orother solvents, solubilizing agents and emulsifiers, such as ethylalcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzylalcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, oils(in particular, cottonseed, groundnut, corn, germ, olive, castor andsesame oils), glycerol, tetrahydrofuryl alcohol, polyethylene glycolsand fatty acid esters of sorbitan, and mixtures thereof. Besides inertdiluents, the oral compositions can also include adjuvants such aswetting agents, emulsifying and suspending agents, sweetening,flavoring, coloring, perfuming and preservative agents.

Suspensions, in addition to the STAMP, may contain suspending agents as,for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitoland sorbitan esters, microcrystalline cellulose, aluminum metahydroxide,bentonite, agar-agar and tragacanth, and mixtures thereof.

Formulations for rectal or vaginal administration may be presented as asuppository, which may be prepared by mixing one or more STAMPs with oneor more suitable nonirritating excipients or carriers comprising, forexample, cocoa butter, polyethylene glycol, a suppository wax or asalicylate, and which is solid at room temperature, but liquid at bodytemperature and, therefore, will melt in the rectum or vaginal cavityand release the active agent. Formulations which are suitable forvaginal administration also include pessaries, tampons, creams, gels,pastes, foams or spray formulations containing such carriers as areknown in the art to be appropriate.

Formulations for the topical or transdermal or epidermal administrationof a STAMP composition include powders, sprays, ointments, pastes,creams, lotions, gels, solutions, patches and inhalants. The activecomponent may be mixed under sterile conditions with a pharmaceuticallyacceptable carrier, and with any preservatives, buffers, or propellantswhich may be required. The ointments, pastes, creams and gels maycontain, in addition to the STAMP composition, excipients, such asanimal and vegetable fats, oils, waxes, paraffins, starch, tragacanth,cellulose derivatives, polyethylene glycols, silicones, bentonites,silicic acid, talc and zinc oxide, or mixtures thereof. Powders andsprays can contain, in addition to the STAMP composition, excipientssuch as lactose, talc, silicic acid, aluminum hydroxide, calciumsilicates and polyamide powder, or mixtures of these substances. Sprayscan additionally contain customary propellants, such aschlorofluorohydrocarbons and volatile unsubstituted hydrocarbons, suchas butane and propane.

The STAMP composition can be alternatively administered by aerosol. Thisis accomplished by preparing an aqueous aerosol, liposomal preparationor solid particles containing the STAMPs. A nonaqueous (e. g.,fluorocarbon propellant) suspension could be used. Sonic nebulizers canalso be used. An aqueous aerosol is made by formulating an aqueoussolution or suspension of the agent together with conventionalpharmaceutically acceptable carriers and stabilizers. The carriers andstabilizers vary with the requirements of the particular compound, buttypically include nonionic surfactants (Tweens, Pluronics, orpolyethylene glycol), innocuous proteins like serum albumin, sorbitanesters, oleic acid, lecithin, amino acids such as glycine, buffers,salts, sugars or sugar alcohols. Aerosols generally are prepared fromisotonic solutions.

Transdermal patches can also be used to deliver STAMP compositions to aninfection site. Such formulations can be made by dissolving ordispersing the agent in the proper medium. Absorption enhancers can alsobe used to increase the flux of the peptidomimetic across the skin. Therate of such flux can be controlled by either providing a ratecontrolling membrane or dispersing the peptidomimetic in a polymermatrix or gel.

Ophthalmic formulations, eye ointments, powders, solutions and the like,are also contemplated as being within the scope of this invention.

Formulations suitable for parenteral administration comprise a STAMP incombination with one or more pharmaceutically-acceptable sterileisotonic aqueous or nonaqueous solutions, dispersions, suspensions oremulsions, or sterile powders which may be reconstituted into sterileinjectable solutions or dispersions just prior to use, which may containantioxidants, buffers, bacterostats, solutes which render theformulation isotonic with the blood of the intended recipient orsuspending or thickening agents.

Examples of suitable aqueous and nonaqueous carriers which may beemployed in the formulations suitable for parenteral administrationinclude water, ethanol, polyols (e. g., such as glycerol, propyleneglycol, polyethylene glycol, and the like), and suitable mixturesthereof, vegetable oils, such as olive oil, and injectable organicesters, such as ethyl oleate. Proper fluidity can be maintained, forexample, by the use of coating materials, such as lecithin, by themaintenance of the required particle size in the case of dispersions,and by the use of surfactants.

Formulations suitable for parenteral administration may also containadjuvants such as preservatives, wetting agents, emulsifying agents anddispersing agents. Prevention of the action of microorganisms may beensured by the inclusion of various antibacterial and antifungal agents,for example, paraben, chlorobutanol, phenol sorbic acid, and the like.It may also be desirable to include isotonic agents, such as sugars,sodium chloride, and the like into the compositions. In addition,prolonged absorption of the injectable pharmaceutical form may bebrought about by the inclusion of agents which delay absorption such asaluminum monostearate and gelatin.

Injectable depot forms are made by forming microencapsule matrices of aSTAMP or in biodegradable polymers such as polylactide-polyglycolide.Depending on the ratio of the STAMP to polymer, and the nature of theparticular polymer employed, the rate of drug release can be controlled.Examples of other biodegradable polymers include poly (orthoesters) andpoly (anhydrides). Depot injectable formulations are also prepared byentrapping the STAMP in liposomes or microemulsions which are compatiblewith body tissue.

In a preferred embodiment of the invention, a STAMP composition isdelivered to a disease or infection site in a therapeutically effectivedose. As is known in the art of pharmacology, the precise amount of thepharmaceutically effective dose of a STAMP that will yield the mosteffective results in terms of efficacy of treatment in a given patientwill depend upon, for example, the activity, the particular nature,pharmacokinetics, pharmacodynamics, and bioavailability of a particularSTAMP, physiological condition of the subject (including race, age, sex,weight, diet, disease type and stage, general physical condition,responsiveness to a given dosage and type of medication), the nature ofpharmaceutically acceptable carriers in a formulation, the route andfrequency of administration being used, and the severity or propensityof a disease caused by pathogenic target microbial organisms, to name afew. However, the above guidelines can be used as the basis forfine-tuning the treatment, e. g., determining the optimum dose ofadministration, which will require no more than routine experimentationconsisting of monitoring the subject and adjusting the dosage.Remington: The Science and Practice of Pharmacy (Gennaro ed. 20.sup.thedition, Williams & Wilkins PA, USA) (2000).

EXAMPLES Example 1 Targeted Killing of Streptococcus mutans by a List ofAntimicrobial Peptides

1.1 Design and construction of STAMPs used in the example and STAMPcomponents (e.g., selectively targeting domains/peptides, antimicrobialpeptides, and linker peptides). STAMPs and their components designed andsynthesized in the examples are listed in Table 1. An initial STAMP wasconstructed by synthesizing full length S. mutans-specific competencestimulating peptide (CSP, 21 amino acids, SEQ ID NO 1, pheromoneproduced by S. mutans) with the antimicrobial peptide G2 (SEQ ID NO3)(16 amino acids, derived from the wide spectrum antimicrobial peptidenovispirin G10 (SEQ ID NO 35)(Eckert et al., 2006) at either theC-terminus or the N-terminus Biological testing of these STAMPs did notreveal any antimicrobial activity. The C-terminal 16 amino acids of CSP,called CSP_(C16) (SEQ ID NO 2), which in previous studies was shown tostill have pheromone activity (Qi et al., 2005)), was used as asubstitute for CSP. Peptides containing CSP_(C16) at either the N orC-terminus of G2, with different linker regions of flexible amino acidsin between, were then synthesized and screened for their antimicrobialactivities (data not shown). From among the potential STAMPs, C16G2 (SEQID NO 4) which consisted of (from N to C terminus) CSP_(C16), a shortlinker peptide (GGG) and G2 (Table 1), was selected for further studydue to its improved minimum inhibitory concentration (MIC), greatlyenhanced killing kinetics and selectivity against S. mutans (whencompared to G2 alone), as disclosed in detail below.

TABLE 1 Peptide sequences (single-letter amino acid code) of selectedSTAMPs, and STAMP components Peptide Properties Amino-acid sequenceSEQ ID No. CSP Pheromone SGSLSTFFRLFNRSFTQALGK  1 C16 TargetingTFFRLFNRSFTQALGK  2 (CSP_(C16)) G2 Antimicrobial KNLRIIRKGIHIIKKY*  3C16G2 STAMP TFFRLFNRSFTQALGKGGGKNLRIIRKGIHIIKKY*  4 M8 or TargetingTFFRLFNR  5 CSP_(M8) M8G2 STAMP TFFRLFNRGGGKNLRIIRKGIHIIKKY*  6 S6L3-33Antimicrobial FKKFWKWFRRF  7 C16-33 STAMPTRRRLFNRSFTQALGKSGGGFKKFWKWFRRF  8 M8-33 STAMP TFFRLFNRSGGGFKKFWKWFRRF 9 1903 Targeting NIFEYFLE 10 BD2.21 Antimicrobial KLFKFLRKHLL 111903-G2 STAMP NIFEYFLEGGGKNLRIIRKGLHIIKKY 12 1903- STAMPNIFEYFLEGGGKLFKFLRKHLL 13 BD2.21 C16- STAMPTFFRLFNRSFTQALGKGGGKLFKFLRKHLL 14 BD2.21 M8- STAMPTFFRLFNRGGGKLFKFLRKHLL 15 BD2.21 1903-33 STAMP NIFEYFLEGGGFKKFWKWFRRF 17*Denotes peptide C-terminal amidation Linker regions between targetingand killing peptides are underlined

To determine whether there was a region within the CSP_(C16) sequencethat was responsible for S. mutans-specific binding, we synthesized aseries of fluorescently labeled CSP_(C16) fragments, and analyzed theirability to bind to S. mutans. The following strategies were utilized indissecting the CSP_(C16) sequence (Table 2): First, a series offragments were constructed by generating deletions of 3 or 4 aminoacids, from the N to C terminus, across the CSP_(C16) sequence (C16-1 toC16-5). Peptides lacking larger portions of the C or N termini ofCSP_(C16) were also synthesized (C16-6 to C16-12). Additionally,peptides with Arg to Asn (a positive to negative change in charge)(C16-4) or Phe to Gly substitutions (for a general decrease inhydrophobicity) (C16-3), as well as peptides representing a 4-residueAla scan of the C16 sequence were constructed (C16-15 to C16-18).Binding assays were performed as described previously (15), and theresults summarized in Table 2. CSP_(C16) and any peptides containingThr6 through Arg13 (TFFRLFNR, SEQ ID NO 5) of CSP were detected as boundto S. mutans UA159 or comD cells while any interruption to this regionvia deletion, substitution or Ala scanning reduced the detectedfluorescent binding compared to CSP_(C16). Some peptides, such as C16-3,-11, -16 and -17, which contained only Thr6-Phe11 and Phe7-Phe11, showedbinding but at a weaker intensity than CSP_(C16) or any other peptideswith the complete Thr6-Arg13 region. Additionally, we observed that Argto Asn or Phe to Gly substitutions were deleterious to cell binding,suggesting that these residues within TFFRLFNR (SEQ ID NO 5, called M8or CSP_(M8)) are required for binding to S. mutans. CSP_(M8) exhibitedlittle or no binding to the other oral streptococci listed in Table 3,indicating that CSP_(M8) may also be capable of specifically binding toS. mutans surfaces. In general, the peptides listed in Table that showedpositive binding to S. mutans can be used as targeting peptides againstS. mutans. These peptides include C16 (SEQ ID NO 1), C16-3 (SEQ ID NO39), C16-4 (SEQ ID NO 40), C16-5 (SEQ ID NO 41), C16-6 (SEQ ID NO 42),C16-11 (SEQ ID NO 47), C16-12 (SEQ ID NO 5), C16-16 (SEQ ID NO 51),C16-17 (SEQ ID NO 52), and C16-18 (SEQ ID NO 53).

TABLE 2 Binding of CSP-fragment peptides to S. mutans.Reported relative binding represents results from both UA159 and comD.Relative S. mutans Peptide Amino acid sequence binding C16 (SEQ ID NO 1)T F F R L F N R S F T Q A L G K +++ 3 to 4 amino acid internal deletionsC16-1 (SEQ ID NO 37) - - - R L F N R S F T Q A L G K -C16-2 (SEQ ID NO 38) T F F - - - N R S F T Q A L G K -C16-3 (SEQ ID NO 39) T F F R L F - - - - T Q A L G K ++C16-4 (SEQ ID NO 40) T F F R L F N R S - - - A L G K +++C16-5 (SEQ ID NO 41) T F F R L F N R S F T Q - - - K +++Terminal deletions C16-6 (SEQ ID NO 42) T F F R L F N R S - - - - - - -+++ C16-7 (SEQ ID NO 43) - - - R L F N R S F T Q A - - - -C16-8 (SEQ ID NO 44) - - - - - - - R S F T Q A L G K -C16-9 (SEQ ID NO 45) T F F - - - - - - - - - - - - - -C16-10 (SEQ ID NO 46) T F F R - - - - - - - - - - - - -C16-11 (SEQ ID NO 47) T F F R L - - - - - - - - - - - +C16-12 (SEQ ID NO 5) T F F R L F N R - - - - - - - - +++ (CSP_(M8))Substitutions C16-13 (SEQ ID NO 48) T G G R L G N R S G T Q A L G K -C16-14 (SEQ ID NO 49) T F F N L F N N S F T Q A L G K - Alanine-scanningC16-15 (SEQ ID NO 50) A A A A L F N R S F T Q A L G K -C16-16 (SEQ ID NO 51) T F F R A A A A S F T Q A L G K +C16-17 (SEQ ID NO 52) T F F R L F N R A A A A A L G K ++C16-18 (SEQ ID NO 53) I F F R L F N R S F T Q A A A A +++

Targeting peptides specific to S. mutans 1903 (SEQ ID NO 10) andantimicrobial peptides S6L3-33 (SEQ ID NO 7) and BD2.21 (SEQ IN NO 13)were developed in the inventors' laboratory (See Example 4). Targetingpeptides were conjugated to antimicrobial peptides via a linker GGG (SEQID NO 17) to yield the STAMPS C16-33 (SEQ ID NO 8), M8-33 (SEQ ID NO 9),1903-BD2.21 (SEQ ID NO. 13), and C16-BD2.21 (SEQ ID NO 14), all of whichwere tested in the similar manner as C16G2 and M8G2.

All peptides listed in Tables 1 and 3 were synthesized usingdouble-coupling cycles by standard 9-fluorenylmethyloxycarbonyl (Fmoc)solid-phase synthesis methods (431A Peptide Synthesizer, AppliedBiosciences or Apex396, Advanced Chemtech) as described previously(Eckert et al., 2006). Completed peptides were cleaved from the resinwith 95% trifluoroacetic acid (TFA) with appropriate scavengers andpurified by reverse-phase high performance liquid chromatography(RP-HPLC) (ACTA Purifier, Amersham) to 90-95%. Peptide molecular masswas determined by matrix-assisted laser desorption/ionization (MALDI)mass spectrometry. Peptides C16G2, G2, and M8G2 were synthesized withamidated C-termini using Fmoc-Tyr(tBu)-Rink Amide MBHA resin (Anaspec).All other peptides were synthesized with the appropriately-substitutedWang resins.

1.2 Fluorescent labeling of peptides and fluorescence microscopy.Aliquots of CSP_(C16) (SEQ ID NO 2), CSP-fragment peptides (Table 2),and C16G2 (SEQ ID NO 4) were labeled with carboxyfluorescein (Sigma) asdescribed previously (Eckert et al., 2006). After peptide cleavage butprior to the bacterial labeling assay, fluorescence intensity per μMpeptide was checked fluorimetrically (λ_(ex)=488 nm, λ_(em)=520 nmVersaFluor, BioRad) and found to be relatively similar (data not shown).To evaluate the level of peptide binding to bacteria, streptococci froman overnight culture (OD₆₀₀ of 0.7-1.0) were washed with phosphatebuffered saline (1×PBS), diluted 1:2 into 1×PBS, and exposed to peptide(16 μM) for 5 min at 25° C. After incubation with peptide, unbound agentwas removed from the bacteria by three cycles of centrifugation (5 min,16,000×g) and resuspension in 1×PBS. Labeling of oral streptococci wasevaluated using brightfield and fluorescence microscopy (Nikon E400) ata 40× magnification. The digital images utilized for thesemi-quantitative binding assessment were acquired with thefactory-supplied software (SPOT, Diagnostics).

1.3 Determination of antimicrobial activity. The general antimicrobialactivity of peptides against planktonic bacteria was determined by a MICassay in TH broth (all oral streptococci) (Qi et al., 2005).

S. mutans, S. gordonii Challis (DL1), and S. sanguinis NY101 strainswere grown in Todd Hewitt (TH, Fisher) broth medium at 37° C. underanaerobic conditions (80% N₂, 10% CO₂, and 10% H₂). S. mutans strainsUA159 (Ajdic et al., 2002), ATCC 25175, and T8 (Rogers, 1975), arewild-type clinical isolates, while comD is a knockout mutant that wasconstructed previously from the wild-type UA140 background (Qi et al.,2005). Luciferase expressing S. mutans strain JM11 was constructed fromUA140 as described (Merritt et al., 2005). Exponentially growingbacterial cells were diluted to ˜1×10⁵ cfu/mL in TH and placed into96-well plates (Fisher). Peptides were then serially diluted and addedto the bacteria. MIC was determined by identifying the concentration ofpeptide that completely inhibited bacterial growth after ˜24 hincubation.

1.4 Determination of bactericidal kinetics. To determine the short termkilling rate and selectivity of C16G2 and G2 we performed time-killexperiments, essentially as described previously (Eckert et al., 2006).S. mutans UA159, S. gordonii, or S. sanguinis were grown to log phaseand diluted to ˜1×10⁵ cfu/mL in growth medium. Under aerobic conditions,25 μM G2 or C16G2 was added to the cell suspension and incubated at 25°C. At 1 min, 10 μL of cell suspension was removed, rescued by dilutioninto growth medium (1:50) and kept on ice. For plating, 20-500 μL ofrescued cells were spread on growth medium agar plates and colonies werecounted after overnight incubation at 37° C. under anaerobic conditions.We considered 60 cfu/mL as the detection limit for this assay. Values ofsurviving cfu/mL were expressed as the ratio of survivors fromC16G2-treated cultures to cfu/mL from samples exposed to G2.

1.5 Examination of antimicrobial activity against single-speciesbiofilms. To initiate biofilm formation, ˜1×10⁷ bacteria per well (fromovernight cultures) were seeded in TH medium (100 μL) to a 96-wellflat-bottom plate. For all streptococci except S. mutans, the medium wassupplemented with 0.5% (w/v) mannose and glucose. S. mutans UA159biofilms were grown with 0.5% (w/v) sucrose. Plates were thencentrifuged briefly to pellet the cells, and bacteria were incubated for3-4 hours at 37° C. for biofilm formation. After incubation, thesupernatant was carefully removed and biofilms were treated with 25 μMpeptide in 1×PBS or 1×PBS alone for 1 min. The peptide solution was thenremoved and 100 μL TH was added to further dilute any remaining peptide.To minimize biofilm loss, cells were briefly centrifuged after THaddition, after which the supernatants were removed and fresh mediumplus appropriate sugars were returned. Cells were then incubatedanaerobically at 37° C. and biofilm growth was monitored over time bymeasuring absorbance at OD₆₀₀ with a microplate spectrophotometer(Benchmark Plus, BioRad).

1.6 Evaluation of antimicrobial activity against bacterial biofilm insaliva. For these experiments, we employed methods similar to thosepreviously described (Bleher et al., 2003). A day prior to the assay,saliva was collected and pooled from 5 adult volunteers in thelaboratory, diluted 1:4 in TH broth and centrifuged 2,000×g for 10 min.The supernatant was then filter sterilized (0.2 μm filter, Nunc) andstored at 4° C. A portion of pooled saliva was also diluted 1:2 in 1×PBSand processed as before. On the day of the assay, overnight cultures ofJM11 and other oral streptococci were normalized to OD₆₀₀ 1.0 and ˜3×10⁶cfu/mL of each species was added to 10 mL of the TH-diluted saliva.Sucrose, mannose, and glucose (1% w/v each) were then added and thesolution mixed. Aliquots (500 μL) of the saliva and bacteria mixturewere then placed into 1.5 mL Eppendorf tubes (Fisher). After a briefcentrifugation (4,000×g, 2 min), the tubes were incubated for 3-4 hoursat 37° C. to form multi-species biofilms. The supernatants were thenremoved and the spent media replaced with 100 μL PBS-diluted saliva(1:2) plus 25 μM (freshly added) peptide. After biofilms were exposed tothe agent for 5 minutes, the PBS-saliva was removed, cells brieflycentrifuged, and 500 μL fresh TH-saliva with sugars was returned. Ateach time point, total biofilm growth was measured by reading absorbanceat OD₆₀₀, and the health of S. mutans within the population examined byrelative luciferase expression (relative light unit, (RLU) production),as described previously (Merritt et al., 2005). Briefly, biofilms wereresuspended by vortex and aspiration and 100 μL of each sampletransferred to a new Eppendorf tube with 25 μL 1 mM D-luciferin (Sigma)solution suspended in 0.1 M citrate buffer, pH 6.0. For the 2 htimepoint, biofilms were stimulated after resuspension by the additionof 1% sucrose 30 min prior to recording luciferase activity. RLUproduction was measured using a TD 20/20 luminometer (Turner Biosystems)and reported values were obtained from the average of 3 independentsamples. The data were plotted as the RLU/OD₆₀₀ over time.

1.7 C16G2 has enhanced antimicrobial activity and specificity againstplanktonic S. mutans cells. To evaluate the antimicrobial activity andgeneral specificity of C16G2, minimum inhibitory concentration (MIC)tests were performed against a panel of bacterial species includingvarious strains of S. mutans and closely related oral streptococci(Gilmore et al., 1987). As shown in Table 3, The MIC values of C16G2ranged from 3-5 M for all S. mutans strains tested, a 4-5 fold increasein antimicrobial activity over the parental antimicrobial peptide G2(12-20 M). In comparison, we observed little difference insusceptibility between G2 and C16G2 (2 fold or less) against S. gordoniiand S. sanguinis.

G10KHc (SEQ ID No 36) did not show much improvement in MIC after 24 hincubation, but displayed greatly enhanced killing kinetics andspecificity against the targeted bacteria during short time exposure(when compared to the untargeted parental antimicrobial peptide (Eckertet al., 2006). Therefore, comparative experiments were performed toexamine the killing ability C16G2 and G2 against its targeted anduntargeted bacteria after a short time exposure. As shown in FIG. 1,with 1 min exposure, C1602 was over 20-fold more active against itstargeted bacterium S. mutans, in comparison to G2, while it exhibited asimilar level of activity as G2 against other oral streptococci tested.These findings provided the first indications that the addition of theCSP_(C16) targeting domain to G2 had resulted in an antimicrobial withselective activity against S. mutans, and not other closely related oralstreptococci.

TABLE 3 MIC of G2-containing STAMPs and STAMP components againstbacteria. MICs represent averages of at least 3 independent experimentswith standard deviations. MIC (μM) of: Strains CSP CSP_(C16) G2 C16G2CSP_(M8) M8G2 S. mutans UA159 50.8 ± 9.3 >60 12.1 ± 4.5 3.0 ± 1.6 >603.25 ± 1.9  25175 >60 >60 14.8 ± 2.0 3.8 ± 0.3 >60 3.5 ± 0.5 T8 >60 >6014.2 ± 1.5 3.7 ± 0.2 >60 nt comD >60 >60 15.3 ± 4.2 5.1 ± 2.4 >60 4.0 ±2.0 Non-mutans streptococci S. gordonii >60 >60  41.3 ± 14.0 23.5 ±7.8  >60  20 ± 5.0 S. sanguinis >60 >60 33.6 ± 7.5 19.1 ± 4.0  >60  15 ±2.5

1.8 C16G2 is also active against biofilm cells. S. mutans predominantlyexist in a biofilm growth state in vivo. It is known in the art thatbiofilm-associated cells are 100-1000 fold more resistant to antibiotics(Donlan et al., 2002). To test whether C16G2 still has activity againstS. mutans biofilms in vitro, biofilm-associated S. mutans, S. gordonii,or S. sanguinis, were treated with 25 M C16G2, G2, CSP, CSP_(C16), or1×PBS, for 1 min, washed, and their re-growth was monitored over time.As shown in FIG. 2, S. gordonii or S. sanguinis biofilms exposed to anyof the peptides tested grew similarly to untreated biofilms afterpeptide addition and removal (FIG. 2A-B). In contrast, S. mutans strainsUA159 (FIG. 2C) as well as T8 and 25175 (data not shown) were severelyinhibited by treatment with C16G2, but were unaffected by treatment withthe other peptides. These results indicate that C16G2 can function as ananti-S. mutans STAMP in a biofilm environment with only a short periodof exposure (1 min), a time-frame which is relevant for clinicaltreatments in the oral cavity (Axelsson & Lindhe, 1987).

1.9 C16G2 can selectively eliminate S. mutans from a mixed speciesbiofilm. In addition to growing as biofilm in vivo, S. mutans are alsoconstantly bathed in saliva as they adhere to the tooth surface. Toexamine whether C16G2 could selectively kill S. mutans under theseconditions, 2 species of non-cariogenic oral streptococci (S. gordoniiand S. sanguinis), were mixed with S. mutans JM11, a strain harboring atranscriptional fusion between luciferase (luc) and the promoter for theconstitutively active gene lactate dehydrogenase (ldh), which has thesame susceptibility to C16G2 as the wild type UA159. JM11 has beenpreviously utilized to measure the fitness of S. mutans populations, anddecreasing relative light unit (RLU) production was shown to stronglycorrelate with reduced cell viability (Merritt et al., 2005). Themixed-species biofilms were formed with saliva, and then peptides (25μM) suspended in saliva were added for 5 min and removed, and thepost-treatment growth of the biofilm was further monitored. The numberof viable S. mutans cells within the biofilm was quantified in parallelby luciferase expression. It was found that C16G2 was able todramatically reduce the S. mutans population within the mixture(reflected in the low luciferase activity) after 5 min exposure,compared to CSP_(C16) and G2 (FIG. 3). Interestingly, even after 120 minpost treatment, the total number of S. mutans within the mixtureremained low (FIG. 3). Taken together, these results indicate that ashort exposure of C16G2 is capable of selectively inhibiting the growthof S. mutans within a multi-species biofilm and in the presence ofsaliva for a minimum of 2 h without harming bystander bacteria oraffecting the overall health of the biofilm.

1.10 Enhanced antimicrobial activity of C16G2 is related to targetedComD-independent binding of CSP_(C16) to S. mutans. To further explorethe mechanism of C16G2 enhanced activity against S. mutans, CSP_(C16)and C16G2 were fluorescently labeled and tested their ability to bind S.mutans and other streptococci. Consistent with observed killingactivity, it was found that CSP_(C16) and C16G2 could specifically bindto S. mutans with a very short time exposure (1-2 min), but not to otheroral streptococci (data not shown). Previous genetic studies suggestedthat CSP may interact with ComD to activate DNA competence in S. mutans(Li et al, 2001). It was unexpected to find that a similar MIC wasobserved for UA159 and the comD strain (Table 3). Consistent with thisobservation, it was also found that fluorescent labeled CSP_(C16) andC16G2 bound to UA159 and the comD mutant in a similar manner, indicatingthat the specific binding ability of CSP to S. mutans is independent ofComD.

1.11 M8G2 has similar anti-S. mutans activity as C16G2. Based on thedata above, it was hypothesized that CSP_(M8) would be sufficient tofunction as an alternative targeting domain for an anti-S. mutans STAMP.To test this hypothesis, CSP_(M8) and G2 were synthesized together toform the STAMP M8G2 (Table 1). As shown in Table 3, M8G2 displayedsimilar MICs against S. mutans and other oral streptococci when comparedto C16G2. Furthermore, single-species biofilm inhibition assays showedthat M8G2, like C16G2, was capable of inhibiting the recovery of S.mutans biofilms (FIG. 4A), but not those of S. sanguinis (FIG. 4B),after 1 min exposure. Since the CSP_(M8) domain is much smaller thanCSP_(C16) and consequently easier to chemically synthesize, theseresults provide a basis for a future design of shorter anti-S. mutansSTAMPs based on CSP_(M8).

1.12 CSP_(C16)/CSP_(M8)-guided STAMPs are functional with an alternativekilling domain. Since the targeting and antimicrobial components of aSTAMP are functionally independent, despite being synthesized as onepeptide (Eckert et al, 2006), it was reasoned that a combination ofCSP_(C16) or CSP_(M8) with a different general antimicrobial peptidecould also result in increased killing activity and selectivity towardsS. mutans when compared with the untargeted killing peptide alone.Therefore, both targeting peptides were conjugated to S6L3-33, a modelwide-spectrum antimicrobial peptide, in a similar arrangement as C16G2and M8G2, to yield the STAMPs C16-33 and M8-33 (Table 1). As shown inTable 4, a 2-3 fold difference in MIC between S6L3-33 and the derivedSTAMPs was observed against S. mutans and the other oral streptococcitested. However, when single-species biofilm studies were conducted(shown in FIG. 5), the S. mutans-selective activity of the STAMPs wasreadily apparent: both C16-33 and M8-33 were capable of retarding S.mutans biofilm growth after a short exposure (FIG. 5A), while culturesof S. sanguinis were not affected by STAMP administration (FIG. 5B).These results indicate a clear enhancement of STAMP activity selectivefor S. mutans biofilms.

TABLE 4 MIC of STAMPs constructed with the S6L3-33 antimicrobial region.MICs represent averages of at least 3 independent experiments withstandard deviations. MIC (μM) Peptide UA159 comD S. sanguinis S.gordonii S6L3-33 7.0 ± 3.0 6.5 ± 2.5 40 ± 7.5 20 ± 5.0 C16-33 2.5 ± 2.12.2 ± 0.5 13.3 ± 5.8  14.6 ± 5.0  M8-33 2.5 ± 2.0 2.5 ± 2.0 20 ± 2.0 10± 2.5

In general, a series of STAMPs which exhibited specificity for S. mutansand not other oral streptococci were synthesized and evaluated. TheSTAMPs were designed for S. mutans-selective activity by incorporatingportions of a natural pheromone produced by these cariogenic bacteria(CSP) as the targeting domain within the linear STAMP peptide. Byexclusively utilizing short (<3 kD) linear peptides for the targetingand antimicrobial regions, we were able to rapidly synthesize andisolate the complete STAMP molecule in once piece via solid-phasechemical methods, a distinct advantage over the recombinant expressionand difficult purification routes necessary to construct the large (>70kD) protein-based targeted antimicrobials that have been described (Qiuet al. 2005). Additionally, the flexibility provided by synthetic routesenabled us to easily increase STAMP diversity by switching betweendifferent combinations of targeting domains (CSP_(M8) and CSP_(C16)) andkilling domains (G2 and S6L3-33) when constructing STAMPs against S.mutans, a task that would otherwise require tedious cloning procedures.

As shown in FIG. 5, CSP_(C16) and CSP_(M8) were able to be conjugated toan alternative antimicrobial peptide (S6L3-33) without the loss of S.mutans selective killing ability. This finding further validates thenotion that the STAMP targeting and antimicrobial domains functionindependently, and are capable of being linked in different combinationswithout the loss of activity. This suggests that future STAMPconstruction will be an unlimited “tunable” process whereby a myriad ofcombinations of antimicrobial, linker and targeting domains can besynthesized in order to select a STAMP with the best specific activity.Furthermore, bacterial STAMP resistance (should it evolve) (Perron etal, 2006) could be easily overcome by switching to alternative,functionally analogous STAMP components, as was done with G2 and S6L3-33in this study. Additionally, peptide pheromones are widely utilized bypathogenic bacteria especially Gram-positive organisms, and thereforerepresent a large and growing pool from which future targeting peptidescould be selected for STAMP construction.

C16G2, M8G2, C16-33 and M8-33 displayed robust specific activity againsttargeted S. mutans bacteria in planktonic cultures and in biofilms withboth single and multi-species, suggesting that we were able to constructa set of functional STAMPs that can discriminate between S. mutans andother non-cariogenic oral streptococci. This selective activity,combined the low cytotoxicity of these peptides (Eckert, et al,unpublished data) indicates that they are useful for anti-cariestherapeutic development. Currently, treatments for S. mutans infectioninclude abstinence from dietary sugars, mechanical removal of the dentalplaque, and general biocide mouthwashes. While all are temporarilyeffective to varied degrees, the unavoidable loss of normal flora thatoccurs with mechanical removal or general antibiotic treatment allows S.mutans to re-establish a niche in the oral cavity without difficulty(Caufield et al., 2000). Therefore, a STAMP with a pathogen-selective(e.g., S. mutans-selective) killing ability is an ideal solution whichselectively kills or reduces the pathogen (e.g., S. mutans) in the floraand allows the normal flora to outgrow affected S. mutans populations.Such an “antibiotic-probiotic” therapeutic will help prevent dentalcaries progression and the high health care costs associated with thisdisease (Anderson & Shi, 2006).

Example 2 Enhancement of Antimicrobial Activity Against Pseudomonasaeruginosa by Co-Administration of G10KHc and Tobramycin

2.1 Pseudomonas aeruginosa is a common opportunistic human pathogen thatis associated with life-threatening acute infections and chronic airwaycolonization during cystic fibrosis. In the US Patent ApplicationPublication NO. 20040137482, novispirin G10, a wide-spectrumantimicrobial peptide was converted into a selectively-targetedantimicrobial peptide (STAMP), G10KHc. Compared to novispirin G10 theG10KHc STAMP had an enhanced killing ability against Pseudomonasmendocina. In this experiment, we explored the antimicrobial activity ofG10KHc against P. aeruginosa and a synergistic enhancement in killingactivity when the G10KHc STAMP was co-administered with tobramycin.

2.2 The G10KHc STAMP and its components. G10Hc STAMP has the followingsequence and components:

G10KHc [targeting peptide-linker peptide- antimicrobial peptide, the linker is underlined]: (SEQ ID NO 36)KKHRKHRKHRKHGGSGGSKNLRRIIRKGIHIIKKYG G10 (Novispirin) antimicrobial peptide:  (SEQ ID NO 35)KNLRRIIRKGIHIIKKYG  Cat-1(also called KH) targeting peptide: (SEQ ID NO 31) KKHRKHRKHRKH  Linker peptide:  (SEQ ID NO 28) GGSGGS.

Solid-phase peptide synthesis of G10 (KNLRRIIRKGIHIIKKYG, SEQ ID NO 35)and G10KHc (KKHRKHRKHRKH-GGSGGS-KNLRRIIRKGIHIIKKYG, SEQ ID NO 36) wascarried out using the Fast-Fmoc (9-fluorenylmethoxycarbonyl) methodologyon a 431A Peptide Synthesizer (Applied Biosciences). Completed peptideswere cleaved from the resin using 95% TFA with the appropriatescavengers. Peptide mass was confirmed by matrix-assisted laserdesorption/ionization (MALDI) mass spectroscopy (Voyager System 4291,Applied Biosystems) and crude peptides purified by reverse-phasehigh-pressure liquid chromatography (HPLC, ACTA Purifier, Amersham)while monitoring UV 215. The mobile phase during HPLC consisted ofwater/acetonitrile (with 0.1% trifluorocetic acid) at a flow rate of 0.5mL/min (Source 15 RPC column, Amersham). The HPLC and MALDI profiles forpurified G10KHc are shown in FIG. 6. Specifically, after purification, asingle peak for G10KHc was observed at retention volume 10.06 mL (FIG.6A), which was found to have the expected mass for G10KHc (predicted4267.08, observed 4267.44) as shown in FIG. 6B.

2.3 Antimicrobial Activities. The general antimicrobial activities ofG10KHc, G10, and tobramycin against clinical isolates of P. aeruginosawere evaluated by minimum inhibitory concentration (MIC) assay aspreviously described (Eckert et al., 2006) and shown in Table 5. MICsare reported in μM, though for familiarity, 1 μM tobramycin=0.468 μg/mL.P. aeruginosa were grown to log phase and adjusted to ˜1×10⁵ cfu/mL inMueller-Hinton (MH) broth and added to 96-well plates. Two-fold serialdilutions of peptide were then added to bacteria and the platesincubated for 18-24 hours at 37° C. MIC was determined as theconcentration of peptide present in the last clear well (no growth). Asexpected, G10KHc was significantly more active against the P. aeruginosaclinical isolates when compared with G10 alone (Student's t test,p=0.001): the MICs for G10KHc ranged from 0.5 to 29 μM (mean 622 μM),compared with the MICs for G10, which ranged from 10 to 60 μM (mean 23.4μM). Since the KH domain (or the Cat-1 peptide) itself does not have anyantimicrobial activity, the increased anti-P. aeruginosa activity ofG10KHc is likely due to the targeted binding ability of KH toPseudomonas spp, as previously reported (Eckert et al., 2006). Incontrast to tobramycin, G10KHc was also effective against aminoglycosideand multiple-antibiotic resistant P. aeruginosa isolated from CFpatients (AGR10, MR15). Additionally, as mucoid P. aeruginosa are oftenassociated with reduced susceptibility to antimicrobial agents, we wereencouraged to find that G10KHc was active against one such strain,PDO300. Overall, G10KHc was not as active as tobramycin against thesensitive isolates examined (typically 1-2 dilution steps lesseffective).

TABLE 5 MICs of tobramycin, G10, and G10KHc against P. aeruginosa laband clinical isolates. The average MIC from at least 3 independentexperiments is shown. The KH targeting domain alone does not have anyantimicrobial activity (data not shown). For reference, 1 μM tobramycin= 0.468 μg/mL. MIC (μM) Strain G10KHc novispirin G10 tobramycin PAO1 623 2.5 PA14 5.5 10 0.7 PAK 5.5 13 2.12 PDO300* 6 45 nt ATCC 15692 6 163.05 ATCC 27583 6 16 1.75 ATCC 10145 4.5 14.5 1.75 ATCC 9027 5.5 15 2.12AGR10 1.1 18 55 MR15 0.5 14 55 S40 29 60 0.4 S60 3.13 30 0.4 S100 1.1 303.5 *mucoid phenotype, nt: not tested

Time-Kill (killing kinetics) experiments were performed essentially asdescribed previously (Eckert et al., 2006). Briefly, P. aeruginosa weregrown to log phase and diluted to ˜1×10⁵ cfu/mL (moderate densityplanktonic cultures) in LB with 30% mouse serum (MP Biomedicals) priorto the addition of 10 μM tobramycin, G10 or G10KHc to the cellsuspensions. At each time point, 10 μL of the culture was removed and P.aeruginosa cells rescued by dilution in 500 μL LB and kept on ice untilplating. Surviving cfu/mL were quantitated after plating on LB agar andincubating overnight at 37° C. under aerobic conditions.

As shown in FIG. 7, the killing kinetics assay revealed that G10KHc hadan obvious improvement in killing versus G10 against P. aeruginosa: 10μM G10KHc treatment of the cultures was associated with a decrease inviable P. aeruginosa (to under 100 cfu/mL by 30 min), while G10 wasineffective over the time course examined. The rate of G10KHcantimicrobial activity was similar to an equimolar dosage of tobramycin(4.68 μg/mL). These results suggest that G10KHc and tobramycin havesimilar potency against clinical isolates as well as lab strains, andthat G10KHc can inhibit the growth of drug-resistant P. aeruginosa.Furthermore, the data indicate that G10KHc appears to require the KHPseudomonas spp targeting domain for effective P. aeruginosa cellkilling: G10 alone showed poor activity unless incubated 18-24 h (Table5).

2.4 Synergistic killing effect of G10KHc and tobramycin. For evaluationof enhanced activity between G10KHc and tobramycin against high densityplanktonic cultures, ATCC 15692 were grown overnight were adjusted to˜1×10⁸ cfu/mL in ddH₂O (pH 7.4) and exposed to 5 μM tobramycin, 5 μMG10KHc or a combination of both agents (a combination of 5 μM tobramycin(2.34 μg/mL) and 5 μM G10KHc or G10). 10 μL of the treated cultures wasrescued by dilution after 24 h and the surviving cfu/mL plated on LB andcounted after growth on LB agar.

As shown in FIG. 8, we observed a clear enhancement in killing activitywhen tobramycin and the STAMP (but not G10) were co-administered.Surviving cfu/mL from co-treated cultures (˜1×10³ cfu/mL) were 5 log₁₀lower than the level recovered from untreated cultures (˜1×10⁸ cfu/mL)or those exposed to either tobramycin or G10KHc (1×10⁷ cfu/mL and ˜1×10⁸cfu/mL, respectively). These results suggest that when applied together,these agents are markedly more effective against planktonic P.aeruginosa than either constituent singly and can eliminate nearly allof a high cell-density culture by 24 hours, even when G10KHc wasadministered at a concentration below the MIC for the tested strain.

2.5 Synergistic killing effect of G10KHc and tobramycin on biofilm. Asynergistic killing effect between tobramycin and G10KHc was alsoobserved against biofilm-associated P. aeruginosa. In this experiment, arotating-disk biofilm reactor system was used for generatingquantitative data on biofilm susceptibility to tobramycin, G10 andG10KHc. The system consisted of a reactor vessel containing 250 mL, ofdiluted trypticase-soy broth (TSB) (1:100) medium. Reactors wereinoculated with overnight cultures (1%, v/v). After static overnightgrowth in TSB, a flow of fresh medium was initiated (dilution rate, 0.7h⁻¹). After 24 h in a flow of medium, the polycarbonate chips withattached biofilm bacteria were aseptically removed from the spinningdisk and washed three times in ddH₂O (pH 7.4) and incubated in 1 mLddH₂O. G10 (100 μg/mL), G10KHc (100 μg/mL), tobramycin (100 μg/mL), or acombination of the two was added as indicated. The chips were thenincubated for 4 or 24 h in 24-well tissue culture plates (Falcon no.353047; Becton Dickinson Labware, Franklin Lakes, N.J.). To estimate thenumber of viable P. aeruginosa remaining, the disks were placed in 1 mLPBS and the cells were dispersed using a tissue homogenizer (BrinkmannInstruments, Westbury, N.Y.) and the total cfu per chip was determinedby serial dilution and plating on LB agar.

As shown in FIG. 9, 100 μg/mL G10KHc or 100 μg/mL tobramycin alone hadvery limited killing effects against P. aeruginosa biofilms after 4 h oreven 24 h. However, the combination of 100 μg/mL G10KHc and 100 μg/mLtobramycin dramatically reduced the level of surviving cfu/mL after 4 h,a 4 log₁₀ improvement in killing ability when compared to either agentalone. More strikingly, no cfu/mL were recovered when the combinedagents were co-incubated with P. aeruginosa for 24 h (a decrease ofnearly 5 log₁₀ from individual applications). These data indicate astrong enhancement in killing activity when G10KHc and tobramycin areused against in vitro P. aeruginosa biofilms. Additionally, theseresults were consistent with FIG. 8, suggesting that G10KHc andtobramycin may be synergistic against P. aeruginosa in planktonic orbiofilm modes of growth, though further experiments are necessary tofully establish synergistic activity.

2.6 G10KHc mediated membrane permeability. The results from FIGS. 8 and9 suggest that the rate of tobramycin cell killing could be increased byG10KHc co-treatment. In the absence of peptide, robust bacterial uptakeof tobramycin is an active process that requires an intact ΔΨ gradient(electric potential of the proton motive force) which is maximizedduring aerobic respiration. This process may be slowed or eliminated inanoxic environments, (such as the interior of biofilms), suggesting thattobramycin diffusion across P. aeruginosa membranes (or lack thereof) iscritical to at least one mechanism of aminoglycoside tolerance in thesebacteria (14, 33, 40). Therefore, due to the membrane-disrupting AMPdomain in G10KHc and its previously described anti-outer membraneactivity (11), it was contemplated that G10KHc was permeabilizing the P.aeruginosa outer and inner membranes, enabling increased tobramycinuptake and leading to the observed synergy.

In order to confirm that G10KHc-membrane disruption could mediatecellular accumulation of a small molecule, overnight cultures of P.aeruginosa were diluted 1:50 in LB and grown to log phase (3-4 h, ˜1×10⁵cfu/mL) prior to mock treatment or treatment with 2 μM G10KHc. After 5min, membrane-compromised cells were stained with propidium iodide (PI)(LIVE/DEAD Baclight Viable Stain, Invitrogen) in the presence or absenceof sub-lethal G10KHc concentrations (2 μM) in accordance with themanufacturer's protocol. PI is a small molecule dye that binds doublestranded DNA and fluoresces red upon excitation and was used as asurrogate for tobramycin as the internalization of an aminoglycoside isnot easily assayable. The dye cannot cross an intact cytoplasmicmembrane and is commonly used for cell viability analysis. Dyeintercalation into DNA (red stain), was detected by fluorescencemicroscopy (Nikon E400) at a 40× magnification. Brightfield and redfluorescence images were collected using the factory default settings(SPOT, Diagnostics). To determine bactericidal activity after peptidetreatment and PI staining, samples prepared in parallel to visualizedcultures were plated on LB agar after 1:5 serial dilutions. Images ofsurviving cfu/mL were taken with a GelDoc (BioRad) using QuantityOnesoftware.

It was expected that G10KHc-induced membrane disruption would lead to anincrease in nucleic acid staining when compared to PI alone. As shown inFIG. 10, bacteria treated with PI alone remained unstained. Incomparison, intracellular PI staining was clearly visible in culturesexposed to PI and G10KHc. Additionally, the amount of red fluorescenceobserved was proportional to the amount and length of G10KHc treatment(data not shown). To ensure that we were not simply staining P.aeruginosa killed by G10KHc, the viable cfu/mL were evaluated from thevisualized cultures. From the serial dilutions shown below the images inFIG. 10, it was clear the number of viable P. aeruginosa recovered wassimilar between cultures treated with PI alone or PI/G10KHc. Overall,these data suggest that a sub-lethal dosage of G10KHc can inducemembrane damage and promote the uptake of small molecules, such astobramycin or PI into metabolically active P. aeruginosa cells.

2.7 Conclusion. In general, In this study, we explored the antimicrobialactivity of G10KHc against P. aeruginosa. G10KHc was found to be highlyactive (equal to tobramycin) against P. aeruginosa clinical isolates.Most interestingly, we observed a synergistic-like enhancement inkilling activity when biofilms and planktonic cultures of P. aeruginosawere co-treated with G10KHc and tobramycin. The data indicate that themechanism of enhanced activity may involve increased tobramycin uptakedue to G10KHc-mediated cell membrane disruption. These results suggestthat G10KHc may be useful against P. aeruginosa during acute and chronicinfection states, especially when co-administered with tobramycin.

P. aeruginosa is a persistent and recurrent opportunistic pathogenresponsible for life-threatening recurrent infections during CF.Frequent isolation of antibiotic-resistant P. aeruginosa suggests thatit is critical that new therapies be developed to inhibit and treat P.aeruginosa colonization of airway mucosal surfaces beforecurrently-prescribed treatment options are no longer effective.

This experiment shows that G10KHc is markedly improved in comparison toits wide-spectrum parent peptide G10, and is similar to that oftobramycin. Additionally, G10KHc is effective against high densityplanktonic cultures and P. aeruginosa biofilms in vitro (FIG. 3-4). Whencompared to tobramycin, G10KHc was nearly 10-fold more effective per μMat reducing biofilm viability (100 μg/mL tobramycin=213 μM, 100 μg/mLG10KHc=23.5 μM). Against high-density planktonic cells, however, 5 μM(2.34 μg/mL) tobramycin alone was markedly more bactericidal than either5 μM G10 or G10KHc after 24 hours (1-2 log₁₀ improvement). Thedifference in tobramycin activity may be linked to the anaerobicenvironment found at the interior of P. aeruginosa biofilms, whichinhibits robust aminoglycoside cellular uptake.

The highest level of anti-P. aeruginosa activity observed in planktonicor biofilm cultures occurred when both agents were applied together.Co-administered tobramycin and G10KHc resulted in a marked enhancementof killing activity: nearly 10,000-fold more bacteria were eliminated byco-treatment than by either agent alone in planktonic and biofilmcultures. Though additive and synergistic anti-P. aeruginosa activityhas been described between an antimicrobial peptide and tobramycin(Saiman et al., 2001), as well as tobramycin plus numerous otherconventional small-molecule antibiotic (Bonacorsi et al., 1999), thecurrent experiment represents the first reported example ofbiofilm-associated P. aeruginosa being synergistically or additivelyeliminated by an aminoglycoside/peptide combination.

Aerosolized tobramycin has been approved for the control of P.aeruginosa infections in CF patients, and not unexpectedly, tobramycinand aminoglycoside-resistant strains of P. aeruginosa and otherorganisms have been isolated from CF sputum. This fact, combined withthe relatively high rate of unpleasant post-treatment dyspnea,bronchospasm, and increased cough, suggests that tobramycin may be bestutilized in a smaller dosage size in combination with another agent. Itis concluded that G10KHc can be a candidate for co-administration due toits engineered Pseudomonas selectivity, and potent antimicrobial effectsagainst P. aeruginosa biofilms and multi-drug andaminoglycoside-resistant strains.

Example 3 Enhanced Stability and Activity of the G10KHc STAMP by UsingD-Amino Acid Enantiomer to Synthesize the STAMP and/or ChemicalAntagonists (e.g., rhDNase)

3.1 Material preparation and methods. G10KHc(KKHRKHRKHRKH-GGSGGS-KNLRRIIRKGIHIIKKYG, SEQ ID NO 36, [targetingdomain-linker-antimicrobial domain]), and the D-enantiomer G10KHc-D weresynthesized by Fast-Fmoc (9-fluorenylmethoxycarbonyl) methodology on a431A Peptide Synthesizer (Applied Biosciences), as described previously(Eckert et al., 2006), using D-amino acids for G10KHc-D purchased fromAnaspec (San Jose, Calif.).

Eight expectorated sputum samples from different patients were obtainedfrom patients with CF at Children's Hospital Los Angeles (Los Angeles,Calif., USA) during routine clinical practice and stored at −80° C.within 1 h of collection. Sputum sample collection for this study wasapproved by the institutional review board at Children's Hospital LosAngeles (CCI #05-00040). All personal identifiers, including age, genderand prognosis, were unknown to our laboratory.

3.2 Activity and stability of G10KHc and G10KHc-D in sputum.Determination of peptide antimicrobial effects or activity in sputum wasinvestigated in a similar manner to previous reports (Sajjan et al.,2001). To assay the activity of G10KHc and G10KHc-D against exogenous P.aeruginosa in sputum, collected sputum samples were diluted 1:10 in 10mM PBS (PBS) and pooled (referred to as pooled sputum). In 100 μL pooledsputum, ATCC 15692 was added to a final concentration of 5×10⁶ cfu/mLprior to 25 μM peptide addition.

In samples examining the effect of protease inhibitors on peptideactivity, pooled sputum samples were pre-treated for 30 min with 1 mMprotease inhibitor, either phenylmethylsulphonylfluoride (PMSF),beta-mercaptoethanol (BME), or ethylenediaminetetraacetic acid (EDTA),(all acquired from Sigma-Aldrich), followed by addition of 25 μM G10KHcand ATCC 15692 (˜5×10⁶ cfu/mL).

Bacteria surviving peptide treatment were rescued by dilution (1:50) ingrowth media at 4 h and kept on ice before appropriate dilution andplating on LB agar supplemented with ampicillin (25 μg/mL) Afterovernight incubation at 37° C., colonies were counted and the survivingcfu/mL quantitated. 100 cfu/mL was considered as the countable limit forall plating procedures. Endogenous organisms already present in thepooled sputum were observed, but were a minority of the populationcompared to the exogenously added cells (less than 1%, data not shown).As a result endogenous and exogenous cfu/mL were not differentiated forthese cultures.

The general antimicrobial effect of G10KHc in sputum samples from CFpatients was evaluated by a killing kinetics assay. As shown in FIG.11A, at 4 h post-peptide addition G10KHc was not active againstexogenously added P. aeruginosa when mixed with pooled sputum samples.This finding was in contrast to G10KHc activity in growth medium, werethe G10KHc STAMP was found to reduce the recoverable cfu/mL over 90%after 30 min of exposure, and eliminate all P. aeruginosa cfu/mL by 2 hof treatment (See Experiment 2).

Considering it likely that the loss of G10KHc activity was due todegradation, the G10KHc STAMP stability in sputum was examined overtime. Stability of peptides in sputum was monitored by HPLC. Briefly,pooled sputum samples were diluted 1:10 in PBS and centrifugedrepeatedly to remove insoluble materials. G10KHc or G10KHc-D (100 μM)was then added to 100 μL diluted pooled sputum (with or without 1 mMPMSF pretreatment for 1 h) and mixed at room temperature. At theindicated timepoints, 20 μL 10% HCl was added to stop peptidedegradation and the sample was filtered twice (0.2 μm nylon, Nunc) priorto injection to the column (Source 15 RPC, Amersham). Water/acetonitrilewith 0.1% trifluorocetic acid was used as the mobile phase and sampleswere eluted with a linear gradient of increasing acetonitrilecomposition (from 10% to ˜35%) at a flow rate of 0.25 mL/min, 11.5 mL ofmobile phase per run. Intact G10KHc and degradation products weremonitored by UV (215 nm) and fractions collected where indicated.Collected fractions from successive runs were pooled and lyophilizedovernight prior to evaluation of antimicrobial activity by the MIC assaydescribed above. HPLC profiles were obtained using the manufacturersprotocol (Unicorn, Amersham), and differentially colored and overlayedusing Photoshop 7.0 (Adobe) for construction of FIG. 11B.

As shown in FIG. 11B, the signature peak (retention volume 10.29) forG10KHc was almost entirely degraded after 30 min of exposure to sputum.Several of the resultant fractions were collected and possibledegradation products were identified by mass spectrometry, none of whichshowed an MIC below 100 μM against several clinical P. aeruginosaisolates (Table 6).

TABLE 6 MIC (μM) of G10KHc, G10KHc-D and sputum-digested products MIC(μM)^(a) ATCC 15692 ATCC 9027 ATCC 27853 Synthesized Peptides:G10KHc^(b) 6 5.5 6 G10KHc-D 15 15 10 HPLC collected fractions^(c): 10.29(G10KHc) 6 6 6 8.50 >100 >100 >100 7.49 >100 >100 >1004.04 >100 >100 >100 ^(a)MIC range of 3 independent experiments ^(b)datapreviously reported included for comparison (6) ^(c)Factions shown inFIG. 1B

It is known in the art that the increased levels of serine proteasespresent in CF sputum. Thus, it was contemplated that we hypothesizedthat this class of proteases were responsible for the rapid G10KHcdegradation observed, and that protease inhibitors could stabilizeG10KHc in sputum and restore antimicrobial function. To examine thispossibility, P. aeruginosa and G10KHc were added to pooled sputumsamples pre-treated with a variety of protease inhibitors, and thesurviving bacteria were quantitated. Samples treated with BME (acysteine protease inhibitor) or EDTA (metalloprotease inhibitor) wereineffective in rescuing G10KHc activity or stability (data not shown).As shown in FIG. 11A, however, P. aeruginosa were effectively killed (areduction of over 3 log₁₀ in surviving cfu/mL) by the G10KHc STAMP insamples pre-treated with the general serine protease inhibitor PMSF. Theinhibitor alone had only a small affect on P. aeruginosa viability.Accordingly, the G10KHc signal from PMSF-treated sputum remained highthrough 4 h when examined by HPLC (FIG. 11B). Overall these dataindicate that G10KHc is active against P. aeruginosa in sputum whenprotected from serine protease degradation.

3.3 D-enantiomer G10KHc STAMP and its activity. Because of the chiralrequirement of most senile proteases (Milton et al., 1992), an allD-amino acid enantiomer of G10KHc, G10KHc-D, was synthesized as analternative means to circumvent protease activity without the use ofinhibitors. G10KHc-D was synthesized by standard solid phase methods asmentioned and confirmed by mass spectrometry.

As shown in FIG. 11A, G10KHc-D reduced the level of recovered P.aeruginosa 3-4 log₁₀ (compared to untreated samples) after 4 h ofpeptide exposure, indicating that G10KHc-D has a level of activity insputum similar to that of L-G10KHc when stabilized. However, theenantiomer was less affective against P. aeruginosa in growth mediumafter 24 h (as evaluated by MIC, Table 6), suggesting that G10KHc-D andL-G10KHc do not have completely identical activities.

3.4 Effect of rhDNase on STAMP activity in sputum. Recombinant humanDNase, which is commonly used during treatment of CF to reduce sputumviscosity and promote airway clearing (Fuchs et al., 1994), was added topooled, concentrated sputum samples to determine if G10KHc/PMSF andG10KHc-D activity could be improved during co-treatment under theseconditions. To determine the effect of rhDNase (Genentech, SanFrancisco, Calif.) on STAMP killing ability, individual sputum sampleswere diluted 1:2 in 100 μg/mL rhDNase, briefly vortexed, and incubatedat room temperature for 10 min. Treated samples were then pooled,followed by 1 mM PMSF addition, where appropriate, and incubation for 1h. 25 μM G10KHc or G10KHc-D was then added with ˜5×10⁶ cfu/mL ATCC 15692and incubated 4 h. Survivors were then rescued and quantitated byplating as described above.

As shown in FIG. 12, we observed a clear enhancement of antimicrobialactivity when rhDNase was utilized in conjunction with G10KHc/PMSF orG10KHc-D (fewer than 5% of untreated cfu/mL remaining), when compared tosamples not treated with rhDNase (˜30% of untreated cfu/mL recovered).P. aeruginosa were not affected by rhDNase treatment alone. Theseresults suggest that the killing effects of G10KHc/PMSF or G10KHc-D insputum can be further enhanced by co-treatment with a sputum mucolyticagent, which may reduce sputum viscosity and enhance peptide diffusion.

3.5 Conclusions. In general, the activity of G10KHc can be extended inexpectorated sputum when protected from proteolytic cleavage, either byconstructing D-version peptides and/or by co-administering a proteaseinhibitor and/or in combination with rhDNase. In particular, it wasfound that robust G10KHc STAMP activity could be maintained inexpectorated sputum if serine protease-dependant digestion associatedwith this fluid was inhibited, either by chemical antagonists or by theconstruction of a D-amino acid enantiomer of G10KHc. Further it wasrevealed that STAMP activity in sputum can be further enhanced whensamples were treated with a combination of peptide and rhDNase. Theresults illustrates the importance of exploring a combination therapy totreat CF, especially if protease-sensitive peptide-based agents, such asG10KHc, are used as alternatives to, or in conjunction with,conventional small-molecule antibiotics.

Experiment 4 Identification of Peptide 1903 and BD2.21 and the STAMPsThereof

The targeting peptide 1903 was obtained by scanning the genomic sequenceof S. mutans UA140. The predicted open reading frames (ORFs) of thepublicly-available genome were examined and those ORFs that encoded forproteins under 50 amino acids were noted and re-examined after scanningthe entire genome. A number of peptides predicted to be encoded by theseORFs were selected, synthesized with fluorescent labels, tested forbinding to S. mutans biofilms. Peptide 1903 showed the binding activityto S. mutans and then was used to synthesize 1903 based STAMPs.

BD2.21 was rationally-designed as part of the “Beta-deletion 2”antimicrobial peptide library. A common alpha helical residuearrangement, HHCCHHCHHH(n), was replaced using mostly positive (C) andhydrophobic (H) residues at the positions indicated. There is somevariability in the pattern of residues we used, and some non-hydrophobicand uncharged residues were incorporated. The replacement was limited to3-5 cationic amino acids per peptide, and 4-7 hydrophobic residues (9 to12 total). The antimicrobial affects of modified peptides were testedand BD2.21 showed an MIC of 5.5 uM against planktonic S mutans. BD2.21was then used to synthesize BD2.21 based STAMP such as 1903-BD2.21having an amino acid sequence of NIFEYFLE-GGG-KLFKFLRKHLL as shown inSEQ ID NO. 13 and C16-BD2.21 having an amino acid sequence ofTFFRLFNRSFTQALGK-GGG-KLFKFLRKHLL as shown in SEQ ID NO 14.

Killing of single-species Streptococcus mutans mature biofilms. S.mutans biofilms were seeded with 10̂5 cells/well and grown overnight with1% sucrose (TH medium) in 48-well plates (final volume 400 μL). Afterincubation, the supernatant was removed from the biofilms and replacedwith 200 μL PBS with 50 μM STAMP. PBS alone was used for the negativecontrol (100% survival) with ethanol as the control for complete killingof the biofilms (0% survival). Biofilms were treated with peptide for 20min, then washed 1× with PBS. To measure biofilm survival, 20 μLCellTiterBlue diluted into 160 μL TH medium was added per well. After3-5 min, the supernatants were removed to a 96 well plate and theabsorbance read at 570 nm. High absorbance at 570 indicated moresubstrate reduction by viable cells remaining in the biofilm. As shownin FIG. 13, the results indicate that C16-BD2.21 and 1903-BD2.21 cankill 66% and 85% of the viable S. mutans within the biofilm,respectively, after a treatment time of only 20 min.

Selectivity of STAMPs against multi-species biofilms of oralstreptococci. To measure selectivity of STAMPs, mixed biofilms wereseeded to 48-well plates. Streptococcus mitis, S. sobrinus, S. gordonii,and S. sanguinis were mixed with S. mutans strain JM11 (spectinomycinresistant) at a 1:1:1:1:10 ratio, total of 10̂5 cells/well. Biofilms weregrown overnight in TH medium with 1% sucrose, 1% dextrose, and 1%mannose, for 18-24 h. Mature biofilms were treated with PBS plus STAMPas described for the single-species biofilm assay, with the samecontrols. After treatment, biofilms were washed 2× in PBS and thenphysically disrupted with a sterile pipette tip in 100 μL PBS per well.Cell suspensions were then serially diluted 10-fold to 10̂-6. Dilutedsuspensions were then plated on TH medium and TH supplemented withspectinomycin, 800 μg/mL. The total amount of biofilm killing (allstreptococci) was determined by counting colonies from TH-only plates.Controls: 100% of untreated corresponds to the number of cfu/mL recordedfrom untreated biofilms, 0% survival was obtained from ethanolsterilized samples. S. mutans killing was determined from quantitatingcolonies on TH-spectinomycin plates, and combined total cfu/mL, wasutilized to calculate the ratio of S. mutans:total population. 1:1 ratioindicates no selectivity.

As shown in FIG. 14, C16-BD2.21 has no impact on the total cfu/mLpopulation, suggesting that non-S. mutans streptococci are not affectedby the STAMP to a significant degree (See FIG. 14(A)). This is confirmedby the observed ratio of surviving S. mutans to total streptococci,which is 0.075 (See FIG. 14 (B)). 1903-BD2.21 also had a selective ratio(well under 1, see FIG. 14 (B)), though had some impact on other oralstreptococci (See FIG. 14 (A)).

TABLE 7 Antimicrobial Peptides Andropin (SEQ ID NO 54)VFIDILDKMENAIHKAAQAGIGIAKPIEKMILPK Apidaecin (SEQ ID NO 55)GNRPVYIPPPRPPHPRL Bacteriocin leucocin A (SEQ ID NO 56)KYYGNGVHCTKSGCSVNWGEAFSAGVHRLANGGNGFW bactenecin (SEQ ID NO 57)RLCRIVVIRVCR Buforin II (SEQ ID NO 58) TRSSRAGLQFPVGRVHRLLRKCathelicidin (human LL-37) (SEQ ID NO 59)LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES Clavanin A (SEQ ID NO 60)VFQFLGKIIHHVGNFVHGFSHVF Cecropin (SEQ ID NO 61)RWKIFKKIEKVGQNIRDGIVKAGPAVAVVGQAATI Cyclic Dodecapeptide (SEQ ID NO 62)RICRIIFLRVCR β-defensin I (human) (SEQ ID NO 63)DFASCHTNGGICLPNRCPGHMIQIGICFRPRVKCCRSW α-defensin (HNP-1) (SEQ ID NO 64)ACYCRIPACIAGERRYGTCIYQGRLWAFCC Gaegurin (SEQ ID NO 65)SLFSLIKAGAKFLGKNLLKQGACYAACKASKQC Histatin (SEQ ID NO 66)DSHEERHHGRHGHHKYGRKFHEKHHSHRGYRSNYLYDN Indolicidin (SEQ ID NO 67)ILPWKWPWWPWRR Magainin II (SEQ ID NO 68) GIGKFLHSAKKFGKAFVGEIMNSMelittin B (SEQ ID NO 69) GIGAVLKVLTTGLPALISWIKRKRQQNisin A (SEQ ID NO 70) ITSISLCTPGCKTGALMGCNMKTATCHCSIHVSKnovispirin G10 (SEQ ID NO 35) KNLRRIIRKGIHIIKKYG Protegrin (SEQ ID NO34)RGGRLCYCRRRFCVCVGR Ranalexin (SEQ ID NO 71) LGGLIKIVPAMICAVTKKCTachyplesin (SEQ ID NO 72) KWCFRVCYRGICYRRCRMaximin H5 (amphibians) (SEQ ID NO 73) ILGPVLGLVSDTLDDVLGILSurfactant Extract 1 (SEQ ID NO 74) DDDDDD DCD-1 (SEQ ID NO 75)SSLLEKGLDGAKKAVGGLGKLGKDAVEDLESVGKGAVHDVKDVLDSV SSL-25 (SEQ ID NO 76)SSLLEKGLDGAKKAVGGLGKLGKDA SSL-23 (SEQ ID NO 77) SSLLEKGLDGAKKAVGGLGKLGKDermaseptinDS5 (SEQ ID NO 78) GLWSKIKTAGKSVAKAAAKAAVKAVTNAVMoricin (insect) (SEQ ID NO 79)AKIPIKAIKTVGKAVGKGLRAINIASTANDVFNFLKPIKKRKABombinin (frog) (SEQ ID NO 80) GIGALSAKGALKGLAKGLAEHFANPleurocidin (white flounder) (SEQ ID NO 81) GWGSFFKKAAHVGKHVGKAALHTYLSMAP29 (sheep) (SEQ ID NO 81) RGLRRLGRKIAHGVKKYGPTVLRIIRIAGPMAP-23 (pig) (SEQ ID NO 83) RIIDLLWRVRRPQKPKFVTVWVRVCP-5h (wasp) (SEQ ID NO 84) FLPIIGKLLSGLL-NH₂Abaecin (honeybee) (SEQ ID NO 85) YVPLPNVPQPGRRPFPTFPGQGPFNPKIKWPQGYDrosocin (fruitfly) (SEQ ID NO 86) GKPRPYSPRPTSHPRPIRVPyrrohocoricin (sap-sucker bug) (SEQ ID NO 87) VDKGSYLPRPTPPRPIYNRNL₁₅K₇ (SEQ ID NO 88) KLLKLLLKLLKLLLKLLLKLLK KLApep (SEQ ID NO 89)KLALKLALKAWKAALKLA-NH₂ D₂A₂₁ (SEQ ID NO 90) FAKKFAKKFKKFAKKFAKFAFAFModelin-1 (SEQ ID NO 91) KLWKKWAKKWLKLWKAW LARL (SEQ ID NO 92)Ac-LARLLARLLARL-Ac YLK-P (SEQ ID NO 93) YKLLKLLLPKLKGLLFKL-NH₂KSL2 (SEQ ID NO 94) KKVVFKFKFK-NH₂ CAM135 (SEQ ID NO 95)GWRLIKKILRVFKGL-NH₂ PGAa (SEQ ID NO 96) GILSKLGKALKKAAKHAAKA-NH₂PGYa (SEQ ID NO 97) GLLRRLRDFLKKIGEKFKKIGY-NH₂

References in the disclosures are listed below and are incorporated intheir entirety.

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1-27. (canceled)
 28. A method of reducing the ratio of livingStreptococcus mutans to total streptococci in a biofilm, said methodcomprising contacting said S. mutans with an amount of a constructeffective to kill an S. mutans, wherein said construct comprises atargeting peptide that binds S. mutans attached to an antimicrobialpeptide, wherein the amino acid sequence of said targeting peptideconsists of a fragment of the competence stimulating peptide (CSP)ranging in length from 8 to 20 amino acids.
 29. The method of claim 28,wherein said fragment comprises the amino acid sequence TFFRLFNR (SEQ IDNO:5).
 30. The method of claim 28, wherein said fragment comprises theamino acid sequence TFFRLFNRSFTQALGK.
 31. The method of claim 28,wherein said fragment consists of the amino acid sequenceTFFRLFNRSFTQALGK.
 32. The method according to any one of claims 28-31,wherein the amino acid sequence of said antimicrobial peptide comprisesa novispirin amino acid sequence or a fragment thereof havingantimicrobial activity.
 33. The method of claim 32, wherein the aminoacid sequence of said antimicrobial peptide comprises the sequenceKNLRIIRKGIHIIKKY (SEQ ID NO:3).
 34. The method of claim 32, wherein theamino acid sequence of said antimicrobial peptide consists of thesequence KNLRIIRKGIHIIKKY (SEQ ID NO:3).
 35. The method of claim 32,wherein the targeting peptide is attached to the antimicrobial peptideby a linker peptide.
 36. The method of claim 35, wherein the targetingpeptide is attached to the antimicrobial peptide by a linker peptide,where the amino acid sequence of said linker peptide is selected fromthe group consisting of GGG (SEQ ID NO:17), AAA (SEQ ID NO:18), SAT (SEQID NO:19), ASA (SEQ ID NO:20), SGG (SEQ ID NO: 21), PYP (SEQ ID NO:22),SGS (SEQ ID NO:23), GGS (SEQ ID NO:24), SPS(SEQ ID NO:25), PSGSP (SEQ IDNO:26), PSPSP (SEQ ID NO:27), and GGSGGS (SEQ ID NO:28).
 37. The methodof claim 32, wherein the amino acid sequence of said construct comprisesthe sequence TFFRLFNRSFTQALGKGGGKNLRIIRKGIHIIKKY.
 38. The method ofclaim 32, wherein the amino acid sequence of said construct consists ofthe sequence TFFRLFNRSFTQALGKGGGKNLRIIRKGIHIIKKY.
 39. The method ofclaim 38, wherein the carboxyl terminus of said antimicrobial peptide isamidated.
 40. The method of claim 38, wherein said biofilm is on an oralsoft tissue or on teeth.
 41. The method of claim 32, wherein thecarboxyl terminus of said antimicrobial peptide is amidated.
 42. Themethod of claim 40, wherein said biofilm is on an oral soft tissue or onteeth.